@text Kinemage Supplement to Branden & Tooze "Introduction to Protein Structure", Second Edition Chapter 5 - ANTIPARALLEL BETA STRUCTURES Contents of file c5Beta.kin: *{Kin 1}* Cu,Zn superoxide dismutase, an antiparallel beta barrel (Fig. 5.1) *{Kin 2}* Retinol-binding protein, an up&down beta barrel (Fig. 5.2-5.4) *{Kin 3}* Neuraminidase, a 6-fold beta-propeller (Fig. 5.6-5.9) *{Kin 4}* Gamma crystallin - repeated domains & Greek key motifs (Fig. 5.10-5.15) *{Kin 5}* Flu hemagglutinin subunit, chains HA1 & HA2 (Fig. 5.20) *{Kin 6}* Flu hemagglutinin jellyroll Greek key beta barrel (Fig. 5.23) *{Kin 7}* Animation of hi- vs low-pH forms of hemagglutinin (Fig. 5.25-5.27) *{Kin 8}* Alkaline proteinase, a 2-sheet parallel beta-helix (Fig. 5.28) *{Kin 9}* P22 tailspike protein, a 3-sheet parallel beta-helix (Fig. 5.29) *{Kin 10}* An exercise in identifying protein folds *{Kinemage 1}* shows a ribbon diagram of Cu,Zn superoxide dismutase (SOD), an 8-stranded antiparallel beta barrel structure with copper and zinc at the active site. View1 matches Fig. 5.1a, with strands pointing up colored skyblue and strands pointing down colored pink, to emphasize that they alternate in direction going around the barrel. View2 looks down the axis of the barrel, as in Fig. 5.1b; turn off "loops" to see the beta structure more clearly. View3 looks from the side of the barrel, as in 5.1c. Beta sheets always twist in a righthanded direction, which makes the strands wind around the barrel axis, so that the back strands are at about a 30 degree angle to the front strands. Some of the connections arch across the barrel, skipping intervening strands, which means that this protein has what is called a Greek key topology (see Kin. 4). *{Kinemage 2}* shows retinol-binding protein (RBP), an 8-stranded antiparallel beta barrel with a simple up&down topology where each strand connects to its nearest neighbor. Upward-pointing strands are in skyblue, downward-pointing strands are in pink, and loops are white. The retinol bound in the hydrophobic interior of the barrel is shown as a space-filling CPK model, with C atoms yellow and O atoms red. Click "Animate" to see the up&down topology of the RBP beta barrel built up one strand at a time from the N- to the C-terminus. Click "2Animate" to see the small changes between apo and holo RBP, including the hydrophobic side chains in the barrel interior which bind the hydrophobic retinol molecule. This cavity is almost completely pre-formed in the apo-protein, with only the two Tyr and Leu side chains near the bottom moving significantly. *{Kinemage 3}* shows one subunit of influenza neuraminidase, made up of six twisted beta sheets that sit radially around a center. Animate, to build up this "propeller" structure one sheet at a time; notice that one of the sheets is formed of one strand from the N-terminus of the chain (yellow) and 3 strands from the C-terminus (skyblue). Turn off "loops", choose View2, and animate again, to accentuate the sheets that form the propeller blades. Turn on "site" to see an N-acetyl glucosamine molecule in the active site at the top end of the propeller stucture (View2 matches Fig. 5.9b). Turn on "SS" to see the 8 disulfide bonds that help "staple" this large structure together. View3 is a close-up of one of the sheets, showing its up&down topology (as in Fig. 5.5). Other "propeller" beta proteins can have as many as 8 sheets or as few as 4; see Kin.3 of file c13SigTr.kin for the 7-bladed propeller of transducin beta. *{Kinemage 4}* shows the Calpha backbone of gamma crystallin, an antiparallel beta protein that is organized into two, well-separated domains related by an approximate 2-fold axis, and into four similar 4-stranded Greek key beta motifs. Each motif has a 4-stranded Greek key topology, where 3 strands are from one sheet and one from the other (see View2, and turn off the other parts temporarily). The colors emphasize the symmetry of the repeats in the structure and sequence: each motif is a different color, and the combination of a pink and a green motif is repeated in each domain. This protein almost certainly evolved by two gene duplication events. View3 looks down the domain 2-fold axis, View4 down the internal 2-fold within domain 1, and View5 turns the whole structure vertical, for viewing in stereo. Choose View6 and turn on "dom2 supr" to see how closely the two domains superimpose on one another. *{Kinemage 5}* shows the long, extended structure of one subunit of the influenza virus hemagglutinin trimer. View1 matches Fig. 5.19, with chain HA1 in red tones and HA2 in blue tones, and the N-terminal part of each chain lighter. Turn on "SS" to see the disulfide bonds both within and between the two chains; disulfides are common in extracellular proteins, both large ones like this viral envelope protein and also small ones such as toxins, hormones, and protease inhibitors. View2 is a close-up of chain HA2, to see the very long alpha-helix that makes trimer contact in the "stem" region. View3 is a close-up of the globular "tip" end of chain HA2, including the beta barrel and the receptor site. View4 shows the four chain termini, all near the membrane end, and emphasizes how the N-terminus of HA1 provides the central strand of the 5-stranded antiparallel beta sheet otherwise made by HA2. *{Kinemage 6}* shows the jellyroll Greek key beta barrel from chain HA1 of influenza virus hemagglutinin. The 8 beta strands are colored corresponding to the way they pair up in the structure - yellow nearest the central hairpin, then blue, then pink, then green. View1 matches Fig. 5.23, while View2 is from one edge of the beta barrel. Animate to see the structure built up in pairs, two strands at a time, out from the central hairpin. *{Kinemage 7}* is an animation of the large pH-dependent conformational rearrangement of the influenza virus hemagglutinin trimer. Only those parts of the structure that were solved at low pH are shown - chain HA1 beta strand I and chain HA2 residues 40-153, joined together by an SS bond. Residues 76-105 in the long alpha-helix are superimposed, while the rest of the structure rearranges very thoroughly, some parts moving more than 100A, bringing the membrane-fusion peptide up to the top of the new long helix. Most parts keep the same local structure, but some parts change from helix to loop or vice-versa. This is not a reversible change, since the low-pH form is more stable. To see the rearrangement more clearly in one monomer, turn off the other two in each form, and animate again. *{Kinemage 8}* shows the 2-sheet parallel beta-helix in domain 2 of bacterial alkaline proteinase, with its bound calciums as yellowtint spheres. The conserved residues of the sequence repeat are labelled in one-letter code for the "Gly" positions and shown as sidechains for the "Asp" and "Leu" positions. 4 Leu and 1 Phe pack between the sheets, 4 Asp and 1 Asn (plus backbone COs) bind the Ca++'s, and 13 glycines (of the 15 possible) are used to make the very tight loops at each end. To see the rest of domain 2, choose View3 and turn "rest" on and "sequence" off; it forms a wider, more twisted, and less regular continuation of the packed beta sheets. *{Kinemage 9}* shows Calpha backbone for the trimer of phage P22 tailspike protein, each subunit of which contains a 3-sheet parallel beta-helix of very similar shape to the ones in pectate lyase. The starting view shows a cross-section of the beta-helix portion, similar to Fig. 5.29b, with the the 3 sheets in yellow, green, and blue. The shape is a squashed triangle, with short 2-residue connections between the yellow and green sheets and longer loops at the other two corners. View2 is a side view similar to Fig. 5.29a (but for tailspike protein rather than pectate lyase). It can be seen that the chain coils monotonically upward in a righthanded spiral (click on a few atoms to check that lower sequence numbers are toward the bottom). Recently a family of proteins (including LpxA) has been found that have lefthanded 3-sheet beta-helices, with an even more triangular cross-section. Choose View3 and turn on "rest" to see the full subunit; it looks rather like a fish from this direction. Turn on the other two subunits, to see the entire tailspike trimer. Notice that the 3 chains intertwine below the beta-helix region; this protein is rock-stable as a native trimer, but it folds up exceedingly slowly and sometimes gets trapped in incorrect aggregates. Choose View4 to see how the beta-helices fit together around the trimer axis. Choose View5 and move Ztrans (by holding down the mouse in the open region of the Ztrans scrollbar) to see the trimer twist as shown by a thin section sliding along the 3-fold axis. *{Kinemage 10}* contains a series of 8 Calpha backbone structures (plus perhaps ligands or SS) of an unfamiliar protein or a domain-sized piece of a protein. Animate to switch between them. Protein 1: To which major tertiary-structure category (Alpha, Alpha/beta, or Beta) does it belong? What is its specific "fold" called? What is the simple rule that makes the site of ligand binding predictable for this type of protein structure? Protein 2: To which major tertiary-structure category does it belong? What is its specific "fold" called? What is the main topological feature diagnostic of this fold? Protein 3: To which major tertiary-structure category does it belong? What is its specific "fold" called? What binds to this protein? Is that usual for this fold? Protein 4: To which major tertiary-structure category does it belong? What is its specific "fold" called? Make a simple diagram of the major secondary-structure feature in one of the internal repeats. Protein 5: This example does not belong to one of the 3 major categories. It is a small irregular protein with very little secondary structure, and its stability depends on a high percentage of SS bridges. Protein 6: To which major tertiary-structure category does it belong? What is its specific "fold" called? Draw a simple diagram of the secondary structure topology. Protein 7: To which major tertiary-structure category does it belong? Ignoring the piece at the bottom (which makes contact with a second subunit), which protein in the textbook does this seem most similar to? Protein 8: To which major tertiary-structure category does it belong? What is its specific "fold" called? Is the Zn near the N-terminal or the C-terminal end of the beta strands? Copyright 1999 Jane S. and David C. Richardson. Permission freely granted for educational, research, and personal use. For program updates and more information, see http://kinemage.biochem.duke.edu. @kinemage 1 @caption (B&T Fig. 5.1) Cu,Zn superoxide dismutase (SOD) antiparallel beta barrel, with up strands in skyblue, down strands in pink, and loops in white. The Cu at the active site and the nearby Zn are shown as balls. View2 looks down the barrel axis and View3 from the side (turn off "loops"). 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-31.771, 11.353, -13.596 {R1 asn 51} width3 -32.255, 11.138, -13.043 {"} width3 -32.748, 10.926, -12.533 {"} width3 -33.258, 10.693, -12.083 {"} width3 -33.792, 10.401, -11.711 {R1 thr 52} width3 -34.356, 10.015, -11.434 {"} width3 -34.939, 9.514, -11.258 {"} width3 -35.456, 8.947, -11.137 {"} width3 -35.802, 8.379, -11.013 {R1 gln 53} width3 -35.875, 7.874, -10.828 {"} width3 -35.601, 7.485, -10.541 {"} width3 -35.031, 7.216, -10.178 {"} width3 -34.248, 7.058, -9.781 {R1 gly 54} width3 -33.333, 7.003, -9.394 {"} width3 -32.366, 7.030, -9.059 {"} width3 -31.422, 7.068, -8.818 {"} width3 -30.572, 7.034, -8.713 {R1 cys 55} width3 -29.890, 6.845, -8.787 {"} width3 -29.435, 6.450, -9.064 {"} width3 -29.219, 5.921, -9.507 {"} width3 -29.244, 5.361, -10.063 {R1 thr 56} width3 -29.508, 4.873, -10.677 {"} width3 -29.989, 4.546, -11.304 {"} width3 -30.571, 4.404, -11.922 {"} width3 -31.116, 4.460, -12.517 {R1 ser 57} width3 -31.483, 4.723, -13.075 {"} width3 -31.569, 5.179, -13.587 {"} width3 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width3 -20.987, 6.947, -28.081 {"} width3 -20.804, 7.121, -28.818 {"} width3 -20.620, 7.165, -29.463 {R1 leu 65 } width3 -20.463, 6.986, -29.967 {"} width3 -20.352, 6.520, -30.295 {"} width3 -20.274, 5.836, -30.462 {"} width3 -20.210, 5.033, -30.498 {R1 ser 66 } width3 -20.137, 4.213, -30.432 {"} width3 -20.036, 3.456, -30.290 {"} width3 -19.890, 2.770, -30.075 {"} width3 -19.682, 2.140, -29.785 {R1 lys 67 } width3 -19.398, 1.556, -29.419 {"} width3 -19.030, 1.006, -28.977 {"} width3 -18.606, 0.499, -28.463 {"} width3 -18.164, 0.042, -27.882 {R1 lys 68 } width3 -17.741, -0.355, -27.240 {"} width3 -17.363, -0.682, -26.546 {"} width3 -17.008, -0.933, -25.824 {"} width3 -16.642, -1.104, -25.101 {R1 his 69 } width3 -16.233, -1.188, -24.404 {"} width3 -15.754, -1.182, -23.757 {"} width3 -15.208, -1.093, -23.163 {"} width3 -14.607, -0.930, -22.618 {R1 gly 70 } width3 -13.960, -0.701, -22.122 {"} width3 -13.283, -0.413, -21.672 {"} width3 -12.602, -0.059, -21.268 {"} width3 -11.948, 0.370, 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{"} width3 -14.114, 2.722, -24.855 {R1 his 78 } width3 -14.658, 3.250, -24.548 {"} width3 -15.149, 3.840, -24.317 {"} width3 -15.592, 4.479, -24.129 {"} width3 -15.999, 5.157, -23.950 {R1 val 79 } width3 -16.378, 5.865, -23.742 {"} width3 -16.732, 6.579, -23.476 {"} width3 -17.031, 7.221, -23.142 {"} width3 -17.236, 7.702, -22.733 {R1 gly 80 } width3 -17.309, 7.930, -22.247 {"} width3 -17.221, 7.852, -21.684 {"} width3 -16.984, 7.553, -21.074 @vectorlist {lp 5-6} color= white {R1 lys 89 } P -8.351, 5.460, 3.244 {"} width3 -8.546, 5.784, 4.123 {"} width3 -8.874, 6.116, 4.938 {"} width3 -9.319, 6.391, 5.598 {R1 asn 90 } width3 -9.865, 6.544, 6.014 {"} width3 -10.484, 6.533, 6.121 {"} width3 -11.105, 6.417, 5.949 {"} width3 -11.641, 6.279, 5.550 {R1 gly 91 } width3 -12.010, 6.202, 4.977 {"} width3 -12.149, 6.251, 4.282 {"} width3 -12.094, 6.421, 3.511 {"} width3 -11.902, 6.692, 2.711 @vectorlist {lp 6-7} color= white {R1 pro 100 } P -9.188, 12.544, -23.742 {"} width3 -9.559, 12.373, 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12.221, -2.780 {R1 ile 33 } P -13.790, 11.170, -1.860 {R2 ile 33 } -15.065, 11.639, -2.238 {R1 ile 33 } P -14.126, 10.684, -1.326 {R2 ile 33 } -15.419, 11.070, -1.668 {R1 thr o 34 } P -14.126, 10.684, -1.326 {R2 thr o 34 } -15.419, 11.070, -1.668 {R1 thr 34 } P -14.475, 10.213, -0.750 {R2 thr 34 } -15.748, 10.517, -1.080 {R1 thr 34 } P -14.841, 9.747, -0.126 {R2 thr 34 } -16.038, 9.979, -0.488 {R1 thr 34 } P -15.200, 9.270, 0.498 {R2 thr 34 } -16.290, 9.438, 0.073 @ribbonlist {ribbon 4} color= pink master= {ribbon} {R1 gly 39 } P -10.393, 0.041, -1.262 {R2 gly 39 } -10.284, 0.842, -1.424 {R1 gly 39 } P -10.065, -0.003, -2.064 {R2 gly 39 } -10.026, 0.860, -2.082 {R1 gly 39 } P -9.871, -0.006, -2.906 {R2 gly 39 } -9.933, 0.888, -2.818 {R1 gly 39 } P -9.834, 0.024, -3.741 {R2 gly 39 } -9.987, 0.943, -3.594 {R1 asp o 40 } P -9.834, 0.024, -3.741 {R2 asp o 40 } -9.987, 0.943, -3.594 {R1 asp 40 } P -9.977, 0.077, -4.523 {R2 asp 40 } -10.170, 1.043, -4.370 {R1 asp 40 } P -10.310, 0.148, -5.217 {R2 asp 40 } -10.464, 1.195, -5.113 {R1 asp 40 } P -10.798, 0.236, -5.840 {R2 asp 40 } -10.851, 1.381, -5.818 {R1 asp 40 } P -11.392, 0.343, -6.418 {R2 asp 40 } -11.315, 1.573, -6.488 {R1 his o 41 } P -11.392, 0.343, -6.418 {R2 his o 41 } -11.315, 1.573, -6.488 {R1 his 41 } P -12.045, 0.472, -6.979 {R2 his 41 } -11.838, 1.742, -7.124 {R1 his 41 } P -12.712, 0.629, -7.545 {R2 his 41 } -12.399, 1.871, -7.729 {R1 his 41 } P -13.363, 0.832, -8.109 {R2 his 41 } -12.964, 1.983, -8.316 {R1 his 41 } P -13.970, 1.106, -8.662 {R2 his 41 } -13.499, 2.111, -8.900 {R1 gly o 42 } P -13.970, 1.106, -8.662 {R2 gly o 42 } -13.499, 2.111, -8.900 {R1 gly 42 } P -14.504, 1.475, -9.191 {R2 gly 42 } -13.966, 2.288, -9.493 {R1 gly 42 } P -14.948, 1.951, -9.690 {R2 gly 42 } -14.339, 2.541, -10.104 {R1 gly 42 } P -15.322, 2.507, -10.167 {R2 gly 42 } -14.638, 2.869, -10.724 {R1 gly 42 } P -15.653, 3.104, -10.638 {R2 gly 42 } -14.891, 3.265, -11.337 {R1 phe o 43 } P -15.653, 3.104, -10.638 {R2 phe o 43 } -14.891, 3.265, -11.337 {R1 phe 43 } P -15.970, 3.706, -11.115 {R2 phe 43 } -15.127, 3.724, -11.925 {R1 phe 43 } P -16.298, 4.281, -11.611 {R2 phe 43 } -15.373, 4.235, -12.480 {R1 phe 43 } P -16.645, 4.826, -12.126 {R2 phe 43 } -15.652, 4.772, -13.015 {R1 phe 43 } P -17.014, 5.345, -12.659 {R2 phe 43 } -15.984, 5.304, -13.548 {R1 his o 44 } P -17.014, 5.345, -12.659 {R2 his o 44 } -15.984, 5.304, -13.548 {R1 his 44 } P -17.411, 5.841, -13.207 {R2 his 44 } -16.389, 5.803, -14.099 {R1 his 44 } P -17.838, 6.314, -13.766 {R2 his 44 } -16.882, 6.243, -14.678 {R1 his 44 } P -18.303, 6.754, -14.318 {R2 his 44 } -17.450, 6.617, -15.264 {R1 his 44 } P -18.810, 7.144, -14.843 {R2 his 44 } -18.076, 6.925, -15.823 {R1 val o 45 } P -18.810, 7.144, -14.843 {R2 val o 45 } -18.076, 6.925, -15.823 {R1 val 45 } P -19.366, 7.468, -15.321 {R2 val 45 } -18.742, 7.165, -16.327 {R1 val 45 } P -19.973, 7.717, -15.738 {R2 val 45 } -19.430, 7.338, -16.753 {R1 val 45 } P -20.618, 7.897, -16.117 {R2 val 45 } -20.134, 7.448, -17.119 {R1 val 45 } P -21.285, 8.018, -16.485 {R2 val 45 } -20.845, 7.503, -17.452 {R1 his o 46 } P -21.285, 8.018, -16.485 {R2 his o 46 } -20.845, 7.503, -17.452 {R1 his 46 } P -21.958, 8.091, -16.871 {R2 his 46 } -21.557, 7.512, -17.778 {R1 his 46 } P -22.622, 8.131, -17.296 {R2 his 46 } -22.265, 7.486, -18.115 {R1 his 46 } P -23.272, 8.169, -17.742 {R2 his 46 } -22.967, 7.460, -18.446 {R1 his 46 } P -23.904, 8.238, -18.181 {R2 his 46 } -23.661, 7.473, -18.743 {R1 gln o 47 } P -23.904, 8.238, -18.181 {R2 gln o 47 } -23.661, 7.473, -18.743 @ribbonlist {ribbon 5} color= sky master= {ribbon} {R1 gly 80 } P -17.286, 7.406, -20.957 {R2 gly 80 } -16.682, 7.699, -21.190 {R1 gly 80 } P -16.905, 7.048, -20.218 {R2 gly 80 } -16.335, 7.256, -20.683 {R1 asp o 81 } P -16.905, 7.048, -20.218 {R2 asp o 81 } -16.335, 7.256, -20.683 {R1 asp 81 } P -16.427, 6.710, -19.529 {R2 asp 81 } -15.875, 6.832, -20.171 {R1 asp 81 } P -15.879, 6.477, -18.929 {R2 asp 81 } -15.323, 6.528, -19.668 {R1 asp 81 } P -15.285, 6.331, -18.403 {R2 asp 81 } -14.726, 6.325, -19.174 {R1 asp 81 } P -14.666, 6.232, -17.923 {R2 asp 81 } -14.136, 6.170, -18.682 {R1 leu o 82 } P -14.666, 6.232, -17.923 {R2 leu o 82 } -14.136, 6.170, -18.682 {R1 leu 82 } P -14.043, 6.138, -17.461 {R2 leu 82 } -13.606, 6.014, -18.187 {R1 leu 82 } P -13.437, 6.013, -16.990 {R2 leu 82 } -13.178, 5.814, -17.683 {R1 leu 82 } P -12.868, 5.841, -16.505 {R2 leu 82 } -12.843, 5.567, -17.157 {R1 leu 82 } P -12.352, 5.610, -16.001 {R2 leu 82 } -12.580, 5.281, -16.594 {R1 gly o 83 } P -12.352, 5.610, -16.001 {R2 gly o 83 } -12.580, 5.281, -16.594 {R1 gly 83 } P -11.908, 5.306, -15.474 {R2 gly 83 } -12.370, 4.959, -15.979 {R1 gly 83 } P -11.550, 4.934, -14.921 {R2 gly 83 } -12.194, 4.617, -15.301 {R1 gly 83 } P -11.263, 4.548, -14.335 {R2 gly 83 } -12.046, 4.292, -14.568 {R1 gly 83 } P -11.028, 4.221, -13.709 {R2 gly 83 } -11.919, 4.030, -13.791 {R1 asn o 84 } P -11.028, 4.221, -13.709 {R2 asn o 84 } -11.919, 4.030, -13.791 {R1 asn 84 } P -10.828, 4.023, -13.039 {R2 asn 84 } -11.809, 3.878, -12.981 {R1 asn 84 } P -10.645, 4.004, -12.320 {R2 asn 84 } -11.708, 3.865, -12.149 {R1 asn 84 } P -10.468, 4.131, -11.563 {R2 asn 84 } -11.596, 3.956, -11.312 {R1 asn 84 } P -10.290, 4.351, -10.782 {R2 asn 84 } -11.449, 4.101, -10.489 {R1 val o 85 } P -10.290, 4.351, -10.782 {R2 val o 85 } -11.449, 4.101, -10.489 {R1 val 85 } P -10.103, 4.611, -9.988 {R2 val 85 } -11.244, 4.247, -9.697 {R1 val 85 } P -9.900, 4.864, -9.194 {R2 val 85 } -10.969, 4.353, -8.946 {R1 val 85 } P -9.693, 5.087, -8.400 {R2 val 85 } -10.650, 4.410, -8.223 {R1 val 85 } P -9.495, 5.262, -7.604 {R2 val 85 } -10.323, 4.418, -7.506 {R1 thr o 86 } P -9.495, 5.262, -7.604 {R2 thr o 86 } -10.323, 4.418, -7.506 {R1 thr 86 } P -9.317, 5.372, -6.804 {R2 thr 86 } -10.026, 4.375, -6.773 {R1 thr 86 } P -9.171, 5.409, -5.998 {R2 thr 86 } -9.785, 4.287, -6.009 {R1 thr 86 } P -9.058, 5.392, -5.183 {R2 thr 86 } -9.587, 4.174, -5.217 {R1 thr 86 } P -8.976, 5.349, -4.354 {R2 thr 86 } -9.412, 4.061, -4.407 {R1 ala o 87 } P -8.976, 5.349, -4.354 {R2 ala o 87 } -9.412, 4.061, -4.407 {R1 ala 87 } P -8.924, 5.308, -3.508 {R2 ala 87 } -9.235, 3.974, -3.591 {R1 ala 87 } P -8.897, 5.292, -2.644 {R2 ala 87 } -9.041, 3.933, -2.775 {R1 ala 87 } P -8.879, 5.301, -1.774 {R2 ala 87 } -8.833, 3.942, -1.954 {R1 ala 87 } P -8.851, 5.330, -0.913 {R2 ala 87 } -8.621, 4.001, -1.119 {R1 asp o 88 } P -8.851, 5.330, -0.913 {R2 asp o 88 } -8.621, 4.001, -1.119 {R1 asp 88 } P -8.795, 5.374, -0.076 {R2 asp 88 } -8.412, 4.110, -0.264 {R1 asp 88 } P -8.703, 5.431, 0.727 {R2 asp 88 } -8.222, 4.268, 0.619 {R1 asp 88 } P -8.612, 5.511, 1.509 {R2 asp 88 } -8.079, 4.484, 1.527 @ribbonlist {ribbon 6} color= pink master= {ribbon} {R1 gly 91 } P -11.581, 6.486, 2.891 {R2 gly 91 } -12.222, 6.897, 2.532 {R1 val o 92 } P -11.581, 6.486, 2.891 {R2 val o 92 } -12.222, 6.897, 2.532 {R1 val 92 } P -11.224, 6.854, 2.097 {R2 val 92 } -12.035, 7.228, 1.755 {R1 val 92 } P -10.857, 7.233, 1.353 {R2 val 92 } -11.794, 7.659, 1.029 {R1 val 92 } P -10.490, 7.612, 0.649 {R2 val 92 } -11.513, 8.149, 0.339 {R1 val 92 } P -10.120, 7.985, -0.036 {R2 val 92 } -11.197, 8.647, -0.336 {R1 ala o 93 } P -10.120, 7.985, -0.036 {R2 ala o 93 } -11.197, 8.647, -0.336 {R1 ala 93 } P -9.745, 8.347, -0.723 {R2 ala 93 } -10.851, 9.103, -1.021 {R1 ala 93 } P -9.369, 8.695, -1.431 {R2 ala 93 } -10.484, 9.481, -1.730 {R1 ala 93 } P -9.019, 9.028, -2.165 {R2 ala 93 } -10.120, 9.798, -2.453 {R1 ala 93 } P -8.730, 9.350, -2.925 {R2 ala 93 } -9.783, 10.088, -3.172 {R1 ile o 94 } P -8.730, 9.350, -2.925 {R2 ile o 94 } -9.783, 10.088, -3.172 {R1 ile 94 } P -8.534, 9.663, -3.712 {R2 ile 94 } -9.501, 10.382, -3.868 {R1 ile 94 } P -8.452, 9.969, -4.523 {R2 ile 94 } -9.293, 10.707, -4.530 {R1 ile 94 } P -8.452, 10.276, -5.339 {R2 ile 94 } -9.143, 11.059, -5.170 {R1 ile 94 } P -8.486, 10.589, -6.139 {R2 ile 94 } -9.033, 11.430, -5.806 {R1 val o 95 } P -8.486, 10.589, -6.139 {R2 val o 95 } -9.033, 11.430, -5.806 {R1 val 95 } P -8.511, 10.917, -6.900 {R2 val 95 } -8.940, 11.812, -6.454 {R1 val 95 } P -8.487, 11.260, -7.606 {R2 val 95 } -8.847, 12.192, -7.131 {R1 val 95 } P -8.408, 11.596, -8.271 {R2 val 95 } -8.742, 12.554, -7.838 {R1 val 95 } P -8.277, 11.897, -8.914 {R2 val 95 } -8.619, 12.877, -8.573 {R1 asp o 96 } P -8.277, 11.897, -8.914 {R2 asp o 96 } -8.619, 12.877, -8.573 {R1 asp 96 } P -8.094, 12.137, -9.557 {R2 asp 96 } -8.469, 13.143, -9.334 {R1 asp 96 } P -7.866, 12.294, -10.218 {R2 asp 96 } -8.289, 13.337, -10.120 {R1 asp 96 } P -7.617, 12.388, -10.911 {R2 asp 96 } -8.096, 13.472, -10.923 {R1 asp 96 } P -7.375, 12.444, -11.647 {R2 asp 96 } -7.912, 13.565, -11.733 {R1 ile o 97 } P -7.375, 12.444, -11.647 {R2 ile o 97 } -7.912, 13.565, -11.733 {R1 ile 97 } P -7.167, 12.487, -12.439 {R2 ile 97 } -7.761, 13.635, -12.541 {R1 ile 97 } P -7.017, 12.540, -13.293 {R2 ile 97 } -7.659, 13.697, -13.342 {R1 ile 97 } P -6.926, 12.601, -14.185 {R2 ile 97 } -7.611, 13.754, -14.137 {R1 ile 97 } P -6.893, 12.666, -15.087 {R2 ile 97 } -7.617, 13.805, -14.932 {R1 val o 98 } P -6.893, 12.666, -15.087 {R2 val o 98 } -7.617, 13.805, -14.932 {R1 val 98 } P -6.915, 12.728, -15.969 {R2 val 98 } -7.678, 13.850, -15.731 {R1 val 98 } P -6.988, 12.783, -16.811 {R2 val 98 } -7.791, 13.888, -16.538 {R1 val 98 } P -7.106, 12.824, -17.619 {R2 val 98 } -7.942, 13.910, -17.353 {R1 val 98 } P -7.262, 12.842, -18.409 {R2 val 98 } -8.113, 13.908, -18.178 {R1 asp o 99 } P -7.262, 12.842, -18.409 {R2 asp o 99 } -8.113, 13.908, -18.178 {R1 asp 99 } P -7.447, 12.831, -19.197 {R2 asp 99 } -8.287, 13.874, -19.012 {R1 asp 99 } P -7.657, 12.785, -19.993 {R2 asp 99 } -8.451, 13.801, -19.854 {R1 asp 99 } P -7.886, 12.704, -20.783 {R2 asp 99 } -8.610, 13.690, -20.702 {R1 asp 99 } P -8.131, 12.592, -21.551 {R2 asp 99 } -8.771, 13.546, -21.551 {R1 pro o 100 } P -8.131, 12.592, -21.551 {R2 pro o 100 } -8.771, 13.546, -21.551 {R1 pro 100 } P -8.389, 12.450, -22.279 {R2 pro 100 } -8.945, 13.372, -22.397 @ribbonlist {ribbon 7} color= sky master= {ribbon} {R1 gly 112 } P -25.794, 15.834, -18.149 {R2 gly 112 } -25.156, 16.147, -17.756 {R1 arg o 113 } P -25.794, 15.834, -18.149 {R2 arg o 113 } -25.156, 16.147, -17.756 {R1 arg 113 } P -25.736, 15.011, -17.880 {R2 arg 113 } -25.075, 15.463, -17.562 {R1 arg 113 } P -25.557, 14.203, -17.576 {R2 arg 113 } -24.954, 14.800, -17.248 {R1 arg 113 } P -25.279, 13.446, -17.230 {R2 arg 113 } -24.796, 14.178, -16.826 {R1 arg 113 } P -24.921, 12.760, -16.837 {R2 arg 113 } -24.593, 13.601, -16.321 {R1 thr o 114 } P -24.921, 12.760, -16.837 {R2 thr o 114 } -24.593, 13.601, -16.321 {R1 thr 114 } P -24.502, 12.166, -16.394 {R2 thr 114 } -24.338, 13.076, -15.758 {R1 thr 114 } P -24.042, 11.676, -15.900 {R2 thr 114 } -24.029, 12.603, -15.161 {R1 thr 114 } P -23.556, 11.260, -15.374 {R2 thr 114 } -23.679, 12.162, -14.554 {R1 thr 114 } P -23.059, 10.880, -14.836 {R2 thr 114 } -23.307, 11.729, -13.956 {R1 met o 115 } P -23.059, 10.880, -14.836 {R2 met o 115 } -23.307, 11.729, -13.956 {R1 met 115 } P -22.566, 10.498, -14.309 {R2 met 115 } -22.933, 11.279, -13.388 {R1 met 115 } P -22.090, 10.080, -13.808 {R2 met 115 } -22.573, 10.792, -12.865 {R1 met 115 } P -21.637, 9.626, -13.327 {R2 met 115 } -22.231, 10.265, -12.376 {R1 met 115 } P -21.212, 9.139, -12.852 {R2 met 115 } -21.908, 9.698, -11.902 {R1 val o 116 } P -21.212, 9.139, -12.852 {R2 val o 116 } -21.908, 9.698, -11.902 {R1 val 116 } P -20.821, 8.623, -12.370 {R2 val 116 } -21.604, 9.091, -11.425 {R1 val 116 } P -20.466, 8.083, -11.874 {R2 val 116 } -21.321, 8.448, -10.933 {R1 val 116 } P -20.146, 7.516, -11.373 {R2 val 116 } -21.057, 7.778, -10.438 {R1 val 116 } P -19.856, 6.922, -10.883 {R2 val 116 } -20.810, 7.096, -9.960 {R1 val o 117 } P -19.856, 6.922, -10.883 {R2 val o 117 } -20.810, 7.096, -9.960 {R1 val 117 } P -19.593, 6.297, -10.418 {R2 val 117 } -20.576, 6.416, -9.516 {R1 val 117 } P -19.354, 5.641, -9.988 {R2 val 117 } -20.357, 5.744, -9.120 {R1 val 117 } P -19.149, 4.963, -9.580 {R2 val 117 } -20.161, 5.071, -8.768 {R1 val 117 } P -18.990, 4.272, -9.173 {R2 val 117 } -19.998, 4.379, -8.451 {R1 his o 118 } P -18.990, 4.272, -9.173 {R2 his o 118 } -19.998, 4.379, -8.451 {R1 his 118 } P -18.888, 3.577, -8.749 {R2 his 118 } -19.880, 3.652, -8.158 {R1 his 118 } P -18.846, 2.889, -8.297 {R2 his 118 } -19.807, 2.881, -7.881 {R1 his 118 } P -18.833, 2.213, -7.849 {R2 his 118 } -19.746, 2.087, -7.615 {R1 his 118 } P -18.810, 1.557, -7.443 {R2 his 118 } -19.653, 1.297, -7.352 {R1 glu o 119 } P -18.810, 1.557, -7.443 {R2 glu o 119 } -19.653, 1.297, -7.352 {R1 glu 119 } P -18.739, 0.926, -7.121 {R2 glu 119 } -19.484, 0.542, -7.089 {R1 glu 119 } P -18.585, 0.328, -6.915 {R2 glu 119 } -19.205, -0.156, -6.828 {R1 glu 119 } P -18.343, -0.224, -6.830 {R2 glu 119 } -18.816, -0.784, -6.613 {R1 glu 119 } P -18.012, -0.716, -6.866 {R2 glu 119 } -18.328, -1.336, -6.495 {R1 lys o 120 } P -18.012, -0.716, -6.866 {R2 lys o 120 } -18.328, -1.336, -6.495 {R1 lys 120 } P -17.593, -1.136, -7.019 {R2 lys 120 } -17.750, -1.805, -6.527 {R1 lys 120 } P -17.091, -1.473, -7.288 {R2 lys 120 } -17.101, -2.184, -6.747 {R1 lys 120 } P -16.533, -1.727, -7.660 {R2 lys 120 } -16.425, -2.476, -7.137 {R1 lys 120 } P -15.952, -1.903, -8.124 {R2 lys 120 } -15.776, -2.686, -7.663 {R1 pro o 121 } P -15.952, -1.903, -8.124 {R2 pro o 121 } -15.776, -2.686, -7.663 {R1 pro 121 } P -15.383, -2.004, -8.667 {R2 pro 121 } -15.206, -2.816, -8.292 {R1 pro 121 } P -14.853, -2.043, -9.276 {R2 pro 121 } -14.756, -2.876, -8.995 {R1 pro 121 } P -14.369, -2.059, -9.933 {R2 pro 121 } -14.411, -2.900, -9.748 @ribbonlist {ribbon 8} color= pink master= {ribbon} {R1 asn 137 } P -18.048, -4.013, -13.352 {R2 asn 137 } -17.601, -4.526, -12.807 {R1 ala o 138 } P -18.048, -4.013, -13.352 {R2 ala o 138 } -17.601, -4.526, -12.807 {R1 ala 138 } P -18.245, -3.841, -12.881 {R2 ala 138 } -17.898, -4.378, -12.219 {R1 ala 138 } P -18.542, -3.617, -12.433 {R2 ala 138 } -18.253, -4.158, -11.692 {R1 ala 138 } P -18.928, -3.360, -11.999 {R2 ala 138 } -18.668, -3.897, -11.218 {R1 ala 138 } P -19.393, -3.089, -11.566 {R2 ala 138 } -19.152, -3.628, -10.779 {R1 gly o 139 } P -19.393, -3.089, -11.566 {R2 gly o 139 } -19.152, -3.628, -10.779 {R1 gly 139 } P -19.924, -2.825, -11.124 {R2 gly 139 } -19.711, -3.385, -10.360 {R1 gly 139 } P -20.505, -2.580, -10.665 {R2 gly 139 } -20.342, -3.186, -9.948 {R1 gly 139 } P -21.108, -2.332, -10.203 {R2 gly 139 } -20.996, -2.988, -9.544 {R1 gly 139 } P -21.698, -2.051, -9.760 {R2 gly 139 } -21.613, -2.733, -9.155 {R1 ser o 140 } P -21.698, -2.051, -9.760 {R2 ser o 140 } -21.613, -2.733, -9.155 {R1 ser 140 } P -22.243, -1.706, -9.353 {R2 ser 140 } -22.133, -2.361, -8.786 {R1 ser 140 } P -22.714, -1.276, -8.996 {R2 ser 140 } -22.511, -1.832, -8.440 {R1 ser 140 } P -23.106, -0.768, -8.670 {R2 ser 140 } -22.760, -1.182, -8.112 {R1 ser 140 } P -23.416, -0.200, -8.349 {R2 ser 140 } -22.908, -0.460, -7.797 {R1 arg o 141 } P -23.416, -0.200, -8.349 {R2 arg o 141 } -22.908, -0.460, -7.797 {R1 arg 141 } P -23.644, 0.410, -8.005 {R2 arg 141 } -22.985, 0.279, -7.488 {R1 arg 141 } P -23.792, 1.048, -7.619 {R2 arg 141 } -23.016, 0.993, -7.181 {R1 arg 141 } P -23.870, 1.706, -7.199 {R2 arg 141 } -23.020, 1.680, -6.881 {R1 arg 141 } P -23.892, 2.378, -6.760 {R2 arg 141 } -23.015, 2.346, -6.595 {R1 leu o 142 } P -23.892, 2.378, -6.760 {R2 leu o 142 } -23.015, 2.346, -6.595 {R1 leu 142 } P -23.870, 3.059, -6.315 {R2 leu 142 } -23.018, 2.999, -6.332 {R1 leu 142 } P -23.820, 3.746, -5.887 {R2 leu 142 } -23.042, 3.644, -6.104 {R1 leu 142 } P -23.762, 4.441, -5.524 {R2 leu 142 } -23.081, 4.283, -5.941 {R1 leu 142 } P -23.718, 5.153, -5.282 {R2 leu 142 } -23.127, 4.916, -5.879 {R1 ala o 143 } P -23.718, 5.153, -5.282 {R2 ala o 143 } -23.127, 4.916, -5.879 {R1 ala 143 } P -23.710, 5.886, -5.217 {R2 ala 143 } -23.171, 5.545, -5.953 {R1 ala 143 } P -23.754, 6.644, -5.366 {R2 ala 143 } -23.206, 6.170, -6.187 {R1 ala 143 } P -23.841, 7.409, -5.687 {R2 ala 143 } -23.244, 6.801, -6.555 {R1 ala 143 } P -23.959, 8.163, -6.118 {R2 ala 143 } -23.300, 7.447, -7.021 {R1 cys o 144 } P -23.959, 8.163, -6.118 {R2 cys o 144 } -23.300, 7.447, -7.021 {R1 cys 144 } P -24.093, 8.886, -6.598 {R2 cys 144 } -23.389, 8.118, -7.549 {R1 cys 144 } P -24.233, 9.564, -7.077 {R2 cys 144 } -23.522, 8.819, -8.103 {R1 cys 144 } P -24.380, 10.210, -7.557 {R2 cys 144 } -23.689, 9.540, -8.666 {R1 cys 144 } P -24.541, 10.844, -8.050 {R2 cys 144 } -23.878, 10.267, -9.220 {R1 gly o 145 } P -24.541, 10.844, -8.050 {R2 gly o 145 } -23.878, 10.267, -9.220 {R1 gly 145 } P -24.721, 11.484, -8.569 {R2 gly 145 } -24.073, 10.984, -9.748 {R1 gly 145 } P -24.917, 12.144, -9.123 {R2 gly 145 } -24.261, 11.679, -10.240 {R1 gly 145 } P -25.094, 12.810, -9.700 {R2 gly 145 } -24.424, 12.347, -10.710 {R1 gly 145 } P -25.212, 13.464, -10.284 {R2 gly 145 } -24.546, 12.984, -11.178 {R1 val 146 } P -25.212, 13.464, -10.284 {R2 val 146 } -24.546, 12.984, -11.178 {R1 val 146 } P -25.226, 14.087, -10.860 {R2 val 146 } -24.607, 13.587, -11.662 {R1 val 146 } P -25.109, 14.667, -11.412 {R2 val 146 } -24.596, 14.157, -12.175 {R1 val 146 } P -24.887, 15.219, -11.931 {R2 val 146 } -24.520, 14.716, -12.685 {R1 val 146 } P -24.599, 15.766, -12.405 {R2 val 146 } -24.389, 15.289, -13.156 {R1 ile 147 } P -24.599, 15.766, -12.405 {R2 ile 147 } -24.389, 15.289, -13.156 {R1 ile 147 } P -24.285, 16.331, -12.827 {R2 ile 147 } -24.217, 15.902, -13.549 {R1 ile 147 } P -23.979, 16.934, -13.189 {R2 ile 147 } -24.017, 16.575, -13.837 {R1 ile 147 } P -23.695, 17.578, -13.498 {R2 ile 147 } -23.803, 17.304, -14.038 {R1 ile 147 } P -23.441, 18.265, -13.762 {R2 ile 147 } -23.592, 18.079, -14.184 {R1 gly 148 } P -23.441, 18.265, -13.762 {R2 gly 148 } -23.592, 18.079, -14.184 {R1 gly 148 } P -23.224, 18.996, -13.990 {R2 gly 148 } -23.402, 18.889, -14.306 {R1 gly 148 } P -23.046, 19.769, -14.188 {R2 gly 148 } -23.241, 19.724, -14.425 {R1 gly 148 } P -22.879, 20.566, -14.347 {R2 gly 148 } -23.085, 20.563, -14.527 {R1 gly 148 } P -22.691, 21.364, -14.457 {R2 gly 148 } -22.901, 21.384, -14.588 {R1 ile 149 } P -22.691, 21.364, -14.457 {R2 ile 149 } -22.901, 21.384, -14.588 {R1 ile 149 } P -22.447, 22.143, -14.507 {R2 ile 149 } -22.657, 22.167, -14.585 {R1 ile 149 } P -22.122, 22.884, -14.488 {R2 ile 149 } -22.328, 22.896, -14.502 @subgroup dominant {Cu,Zn} @spherelist {Cu} color= gold radius= 1.0 {Cu cu o 1} -20.628 2.496 -14.6 @spherelist {Zn} color= bluetint radius= 1.0 {Zn zn o 2} -17.865 1.322 -20.093 @kinemage 2 @caption Retinol-binding protein (RBP), an antiparallel beta barrel of 8 strands with a simple up&down topology. Up strands are skyblue, down strands are pink, and the retinol bound inside the barrel is shown as CPK spheres (C yellow, O red). Animate to see RBP built up from N to C terminus. Click "2animate" for apo-holo changes and retinol-binding side chains, in stick-figure form. (from PDB files 1BRP, 1BRQ) @onewidth @viewid {front} @zoom 1.06 @zslab 179 @center 17.301 43.982 -36.629 @matrix -0.282814 .954823 -.091295 -.182543 .039862 .982386 .941643 .294499 .163028 @2viewid {top} @2zoom 1.0 @2zslab 178 @2center 14.542 47.192 -37.514 @2matrix -0.30349 -.03758 .95209 -.00459 -.99915 -.0409 .95282 -.01678 .30306 @3viewid {ret-bdg} @3zoom 1.61 @3zslab 89 @3center 18.205 51.290 -35.885 @3matrix 0.14706 .96996 -.19378 -.83467 .01657 -.5505 -.53075 .2427 .81203 @group dominant {RBP} animate @subgroup {Calphas} @vectorlist {lp 0} color= white master= {loops} {ca glu 1} P 23.324 21.586 -29.53 {ca arg 2} 23.124 25.293 -29.08 {ca asp 3} 20.531 27.049 -27.178 {ca cys 4} 18.326 29.812 -28.442 {ca arg 5} 17.773 31.413 -25.108 {ca val 6} 18.379 35.124 -25.185 {ca ser 7} 20.40 35.151 -21.944 {ca ser 8} 22.762 32.815 -23.671 {ca phe 9} 23.562 34.999 -26.661 {ca arg 10} 27.107 36.342 -26.667 {ca val 11} 27.696 40.017 -27.201 {ca lys 12} 30.628 42.061 -28.224 {ca glu 13} 33.075 41.796 -25.366 {ca asn 14} 34.646 45.169 -24.407 {ca phe 15} 32.488 47.132 -26.958 {ca asp 16} 33.787 50.599 -27.865 {ca lys 17} 31.447 53.403 -28.744 {ca ala 18} 33.811 55.746 -30.342 {ca arg 19} 35.311 53.012 -32.447 {ca phe 20} 31.71 52.314 -33.631 {ca ser 21} 30.607 55.872 -34.552 @vectorlist {b 1} color=pink master= {beta} {ca ser 21} 30.607 55.872 -34.552 {ca gly 22} 29.997 56.659 -38.175 {ca thr 23} 27.853 55.561 -40.989 {ca trp 24} 26.55 52.115 -41.33 {ca tyr 25} 24.552 50.546 -44.049 {ca ala 26} 21.938 47.931 -43.495 {ca met 27} 22.731 44.944 -45.704 {ca ala 28} 20.40 42.477 -44.098 {ca lys 29} 17.406 42.429 -41.792 {ca lys 30} 15.355 40.057 -39.733 {ca asp 31} 12.031 41.855 -39.244 {ca pro 32} 10.082 41.913 -36.021 {ca glu 33} 6.359 41.693 -35.719 {arw b1}P 8.488 40.385 -35.804 {ca glu 33} 6.359 41.693 -35.719 {arw b1} 8.306 43.242 -35.965 @vectorlist {lp 1} color= white master= {loops} {ca glu 33} 6.359 41.693 -35.719 {ca gly 34} 4.429 44.565 -37.15 {ca leu 35} 5.72 47.851 -38.459 {ca phe 36} 9.29 48.181 -39.467 {ca leu 37} 11.777 49.821 -41.785 {ca gln 38} 11.603 48.238 -45.278 @vectorlist {b 2} color=sky master= {beta} {ca gln 38} 11.603 48.238 -45.278 {ca asp 39} 14.824 48.967 -47.224 {ca asn 40} 17.428 51.667 -47.949 {ca ile 41} 18.358 51.714 -44.324 {ca val 42} 21.231 53.829 -43.235 {ca ala 43} 22.209 54.459 -39.709 {ca glu 44} 24.653 57.032 -38.384 {ca phe 45} 26.062 56.418 -34.911 {ca ser 46} 27.533 59.117 -32.642 {ca val 47} 28.708 59.496 -28.998 {ca asp 48} 29.201 62.773 -26.966 {ca glu 49} 31.667 64.299 -24.44 {arw b2}P 31.117 64.041 -26.865 {ca glu 49} 31.667 64.299 -24.440 {arw b2} 29.591 62.932 -24.705 @vectorlist {lp 2} color= white master= {loops} {ca glu 49} 31.667 64.299 -24.44 {ca thr 50} 29.559 62.46 -21.874 {ca gly 51} 30.008 59.003 -23.34 @vectorlist {b 3} color=pink master= {beta} {ca gly 51} 30.008 59.003 -23.34 {ca gln 52} 26.446 58.686 -24.435 {ca met 53} 25.954 57.13 -27.796 {ca ser 54} 23.136 58.091 -30.107 {ca ala 55} 22.136 57.85 -33.717 {ca thr 56} 19.881 58.667 -36.566 {ca ala 57} 18.481 56.262 -39.064 {ca lys 58} 16.468 56.456 -42.201 {ca gly 59} 14.789 54.133 -44.66 {ca arg 60} 11.666 53.432 -46.643 {ca val 61} 8.667 52.438 -44.56 {ca arg 62} 5.471 51.227 -46.113 {ca leu 63} 2.797 52.928 -44.084 {ca leu 64} -0.624 51.291 -44.242 {arw b3}P 1.560 51.358 -43.027 {ca leu 64} -0.624 51.291 -44.242 {arw b3} 0.883 52.990 -45.286 @vectorlist {lp 3} color= white master= {loops} {ca leu 64} -0.624 51.291 -44.242 {ca asn 65} -1.88 50.522 -47.727 @vectorlist {b 4} color=sky master= {beta} {ca asn 65} -1.88 50.522 -47.727 {ca asn 66} 1.017 51.682 -49.914 {ca trp 67} 2.059 55.068 -48.712 {ca asp 68} 5.825 55.041 -48.703 {ca val 69} 7.473 57.481 -46.46 {ca cys 70} 11.152 58.027 -46.013 {ca ala 71} 11.285 57.908 -42.282 {ca asp 72} 14.095 59.636 -40.339 {ca met 73} 14.48 58.385 -36.817 {ca val 74} 16.407 59.164 -33.748 {ca gly 75} 17.565 56.761 -31.132 {ca thr 76} 19.391 57.461 -27.894 {ca phe 77} 21.266 54.678 -26.15 {ca thr 78} 21.093 54.166 -22.45 {ca asp 79} 23.966 52.061 -21.197 {arw b4}P 23.189 54.388 -21.676 {ca asp 79} 23.966 52.061 -21.197 {arw b4} 21.626 52.017 -22.077 @vectorlist {lp 4} color= white master= {loops} {ca asp 79} 23.966 52.061 -21.197 {ca thr 80} 23.718 48.95 -19.09 {ca glu 81} 26.136 46.861 -17.026 {ca asp 82} 26.968 45.192 -20.27 {ca pro 83} 28.953 47.405 -22.643 {ca ala 84} 27.527 45.708 -25.676 @vectorlist {b 5} color=pink master= {beta} {ca ala 84} 27.527 45.708 -25.676 {ca lys 85} 24.064 46.077 -24.384 {ca phe 86} 21.977 49.188 -24.297 {ca lys 87} 18.52 50.34 -23.941 {ca met 88} 17.538 52.333 -26.994 {ca lys 89} 14.821 54.999 -26.772 {ca tyr 90} 13.752 55.951 -30.291 {ca trp 91} 11.351 58.262 -31.96 {ca gly 92} 10.875 59.846 -35.346 {arw b5}P 10.341 57.864 -33.919 {ca gly 92} 10.875 59.846 -35.346 {arw b5} 11.926 60.107 -33.093 @vectorlist {lp 5} color= white master= {loops} {ca gly 92} 10.875 59.846 -35.346 {ca val 93} 11.262 63.537 -36.19 {ca ala 94} 7.679 63.897 -37.285 {ca ser 95} 5.387 62.96 -34.418 {ca phe 96} 3.318 60.395 -36.277 {ca leu 97} 6.144 58.06 -37.062 @vectorlist {b 6} color=sky master= {beta} {ca leu 97} 6.144 58.06 -37.062 {ca gln 98} 6.721 55.341 -34.42 {ca lys 99} 8.232 55.872 -30.99 {ca gly 100} 9.469 53.135 -28.628 {ca asn 101} 12.195 51.711 -26.296 {ca asp 102} 14.126 48.74 -27.599 {ca asp 103} 16.88 46.632 -26.248 {ca his 104} 19.778 47.138 -28.605 {ca trp 105} 22.674 44.774 -28.352 {ca ile 106} 25.861 44.624 -30.339 {ca val 107} 26.348 41.026 -31.057 {ca asp 108} 29.587 41.623 -32.813 {ca thr 109} 31.335 44.205 -34.929 {ca asp 110} 34.862 44.98 -35.981 {arw b6}P 32.782 43.721 -36.562 {ca asp 110} 34.862 44.980 -35.981 {arw b6} 33.102 45.395 -34.255 @vectorlist {lp 6} color= white master= {loops} {ca asp 110} 34.862 44.98 -35.981 {ca tyr 111} 34.253 48.642 -36.127 {ca asp 112} 35.574 48.843 -39.659 {ca thr 113} 33.556 46.402 -41.719 {ca tyr 114} 30.624 44.815 -40.086 @vectorlist {b 7} color=pink master= {beta} {ca tyr 114} 30.624 44.815 -40.086 {ca ala 115} 28.28 44.82 -37.242 {ca val 116} 25.573 42.462 -36.19 {ca gln 117} 22.798 43.847 -34.074 {ca tyr 118} 20.02 42.025 -32.295 {ca ser 119} 16.925 42.998 -30.455 {ca cys 120} 14.446 40.919 -28.567 {ca arg 121} 11.235 42.795 -27.896 {ca leu 122} 9.315 39.978 -26.271 {arw b7}P 10.857 41.904 -25.869 {ca leu 122} 9.315 39.978 -26.271 {arw b7} 9.855 41.107 -28.435 @vectorlist {lp 7} color= white master= {loops} {ca leu 122} 9.315 39.978 -26.271 {ca leu 123} 10.657 36.786 -24.642 {ca asn 124} 8.962 33.409 -24.719 {ca leu 125} 8.082 31.551 -21.554 {ca asp 126} 11.032 29.382 -22.315 {ca gly 127} 13.644 32.065 -22.37 {ca thr 128} 13.778 32.203 -26.15 {ca cys 129} 12.735 35.295 -28.058 {ca ala 130} 9.174 35.608 -29.10 @vectorlist {b 8} color=sky master= {beta} {ca ala 130} 9.174 35.608 -29.10 {ca asp 131} 9.701 38.792 -31.023 {ca ser 132} 13.086 39.945 -32.278 {ca tyr 133} 14.87 41.836 -35.058 {ca ser 134} 18.437 41.801 -36.269 {ca phe 135} 20.395 44.023 -38.479 {ca val 136} 23.506 43.119 -40.336 {ca phe 137} 25.517 46.30 -40.859 {ca ser 138} 28.153 47.184 -43.371 {ca arg 139} 30.473 50.113 -43.552 {arw b8}P 30.176 47.786 -42.687 {ca arg 139} 30.473 50.113 -43.552 {arw b8} 28.230 49.233 -44.219 @vectorlist {lp 8} color= white master= {loops} {ca arg 139} 30.473 50.113 -43.552 {ca asp 140} 30.384 49.766 -47.336 {ca pro 141} 27.152 50.252 -49.22 {ca asn 142} 28.366 47.513 -51.489 {ca gly 143} 28.382 44.682 -48.995 {ca leu 144} 30.995 42.892 -46.936 {ca pro 145} 34.11 40.98 -47.739 {ca pro 146} 33.851 37.243 -47.887 {ca glu 147} 35.821 37.121 -44.698 {ca ala 148} 33.41 39.357 -42.977 {ca gln 149} 30.417 37.709 -44.486 {ca lys 150} 31.534 34.405 -43.133 {ca ile 151} 31.617 35.487 -39.499 {ca val 152} 28.383 37.256 -39.86 {ca arg 153} 26.692 34.176 -41.183 {ca gln 154} 28.149 32.436 -38.165 {ca arg 155} 26.474 34.988 -35.866 {ca gln 156} 23.196 34.85 -37.671 {ca glu 157} 23.365 31.163 -36.807 {ca glu 158} 24.229 31.606 -33.156 {ca leu 159} 21.165 33.906 -32.90 {ca cys 160} 18.857 31.171 -34.109 {ca leu 161} 17.982 33.521 -36.955 {ca ala 162} 20.008 32.267 -39.897 {ca arg 163} 17.808 31.855 -42.787 {ca gln 164} 15.412 34.35 -41.508 {ca tyr 165} 17.043 37.409 -42.863 {ca arg 166} 16.353 39.276 -46.006 {ca leu 167} 18.638 41.399 -48.116 {ca ile 168} 18.029 45.12 -47.907 {ca val 169} 18.199 47.317 -50.883 {ca his 170} 19.64 50.777 -51.265 {ca asn 171} 18.285 51.909 -54.614 {ca gly 172} 18.277 55.63 -53.918 {ca tyr 173} 14.88 55.94 -52.241 {ca cys 174} 15.811 58.058 -49.214 @subgroup {retinol} master= {retinol} @balllist {O} color= red radius= .2 {or rtl 176} 6.45 54.399 -38.575 @vectorlist {retinol} color=yellow {c16 rtl 176} P 18.107 50.057 -34.997 {c1 rtl 176} 18.205 51.29 -35.885 {c2 rtl 176} 19.642 51.577 -35.44 {c3 rtl 176} 19.76 52.84 -34.598 {c4 rtl 176} 18.737 53.858 -35.071 {c5 rtl 176} 17.33 53.31 -34.876 {c18 rtl 176} 16.662 54.252 -33.891 {c1 rtl 176} P 18.205 51.29 -35.885 {c6 rtl 176} 17.066 51.992 -35.151 {c7 rtl 176} 15.653 51.612 -35.10 {c8 rtl 176} 14.853 52.31 -35.977 {c9 rtl 176} 13.471 51.806 -36.06 {c1 rtl 176} 12.765 52.511 -37.001 {c11 rtl 176} 11.368 52.078 -37.099 {c12 rtl 176} 10.679 52.932 -37.929 {c13 rtl 176} 9.215 52.784 -37.922 {c14 rtl 176} 8.687 53.84 -38.622 {c15 rtl 176} 7.362 53.574 -39.168 {or rtl 176} 6.45 54.399 -38.575 {c1 rtl 176} P 18.205 51.29 -35.885 {c17 rtl 176} 18.151 50.878 -37.339 {c9 rtl 176} P 13.471 51.806 -36.06 {c19 rtl 176} 13.246 50.564 -35.205 {c13 rtl 176} P 9.215 52.784 -37.922 {c2 rtl 176} 8.811 51.391 -38.389 {c5 rtl 176} P 17.33 53.31 -34.876 {c6 rtl 176} 17.066 51.992 -35.151 @subgroup {retinol} master= {CPK} @spherelist {O} color= red radius= 1.4 {or rtl 176} 6.45 54.399 -38.575 @spherelist {C} color=yellow radius= 1.5 {c1 rtl 176} 18.205 51.29 -35.885 {c2 rtl 176} 19.642 51.577 -35.44 {c3 rtl 176} 19.76 52.84 -34.598 {c4 rtl 176} 18.737 53.858 -35.071 {c5 rtl 176} 17.33 53.31 -34.876 {c6 rtl 176} 17.066 51.992 -35.151 {c7 rtl 176} 15.653 51.612 -35.10 {c8 rtl 176} 14.853 52.31 -35.977 {c9 rtl 176} 13.471 51.806 -36.06 {c1 rtl 176} 12.765 52.511 -37.001 {c11 rtl 176} 11.368 52.078 -37.099 {c12 rtl 176} 10.679 52.932 -37.929 {c13 rtl 176} 9.215 52.784 -37.922 {c14 rtl 176} 8.687 53.84 -38.622 {c15 rtl 176} 7.362 53.574 -39.168 {c16 rtl 176} 18.107 50.057 -34.997 {c17 rtl 176} 18.151 50.878 -37.339 {c18 rtl 176} 16.662 54.252 -33.891 {c19 rtl 176} 13.246 50.564 -35.205 {c2 rtl 176} 8.811 51.391 -38.389 @subgroup {labels} @labellist {lbl} color=sea master= {labels} {C-t} 15.811 58.058 -49.214 {N-t} 23.324 21.586 -29.53 @group dominant { strand} animate @vectorlist {lp0} instance= {lp 0} @group dominant {1 strand} animate @subgroup {str 1} @vectorlist {lp0} instance= {lp 0} @vectorlist {b1} instance= {b 1} @vectorlist {lp1} instance= {lp 1} @group dominant {2 strands} animate @subgroup {str1} instance= {str 1} @subgroup {str 2} @vectorlist {b2} instance= {b 2} @vectorlist {lp2} instance= {lp 2} @group dominant {3 strands} animate @subgroup {str1} instance= {str 1} @subgroup {str2} instance= {str 2} @subgroup {str 3} @vectorlist {b3} instance= {b 3} @vectorlist {lp3} instance= {lp 3} @group dominant {4 strands} animate @subgroup {str1} instance= {str 1} @subgroup {str2} instance= {str 2} @subgroup {str3} instance= {str 3} @subgroup {str 4} @vectorlist {b4} instance= {b 4} @vectorlist {lp4} instance= {lp 4} @group dominant {5 strands} animate @subgroup {str1} instance= {str 1} @subgroup {str2} instance= {str 2} @subgroup {str3} instance= {str 3} @subgroup {str4} instance= {str 4} @subgroup {str 5} @vectorlist {b5} instance= {b 5} @vectorlist {lp5} instance= {lp 5} @group dominant {6 strands} animate @subgroup {str1} instance= {str 1} @subgroup {str2} instance= {str 2} @subgroup {str3} instance= {str 3} @subgroup {str4} instance= {str 4} @subgroup {str5} instance= {str 5} @subgroup {str 6} @vectorlist {b6} instance= {b 6} @vectorlist {lp6} instance= {lp 6} @group dominant {7 strands} animate @subgroup {str1} instance= {str 1} @subgroup {str2} instance= {str 2} @subgroup {str3} instance= {str 3} @subgroup {str4} instance= {str 4} @subgroup {str5} instance= {str 5} @subgroup {str6} instance= {str 6} @subgroup {str 7} @vectorlist {b7} instance= {b 7} @vectorlist {lp7} instance= {lp 7} @group dominant {8 strands} animate @subgroup {ca} instance= {Calphas} @subgroup {lbl} instance= {labels} @group dominant {BRQ - apo} 2animate @subgroup {Calphas} @vectorlist {lp 0a} color= white master= {loops} {ca glu 1}P 23.65 21.705 -29.321 {ca arg 2} 23.474 25.477 -29.356 {ca asp 3} 21.156 27.317 -27.054 {ca cys 4} 18.435 29.59 -28.176 {ca arg 5} 17.786 31.401 -24.912 {ca val 6} 18.46 35.142 -24.793 {ca ser 7} 20.58 35.317 -21.673 {ca ser 8} 23.008 33.08 -23.588 {ca phe 9} 23.564 35.24 -26.625 {ca arg 10} 27.096 36.48 -26.69 {ca val 11} 27.844 40.091 -27.24 {ca lys 12} 30.742 42.328 -28.098 {ca glu 13} 33.215 42.041 -25.276 {ca asn 14} 34.632 45.459 -24.344 {ca phe 15} 32.291 47.324 -26.78 {ca asp 16} 33.775 50.671 -27.873 {ca lys 17} 31.374 53.454 -28.785 {ca ala 18} 33.88 55.823 -30.231 {ca arg 19} 35.187 53.154 -32.539 {ca phe 20} 31.552 52.387 -33.541 {ca ser 21} 30.494 55.887 -34.51 @vectorlist {b 1a} color=pinktint master= {beta} {ca ser 21}P 30.494 55.887 -34.51 {ca gly 22} 29.963 56.724 -38.075 {ca thr 23} 27.93 55.68 -41.024 {ca trp 24} 26.557 52.15 -41.319 {ca tyr 25} 24.55 50.711 -44.201 {ca ala 26} 21.986 48.085 -43.528 {ca met 27} 22.607 44.974 -45.652 {ca ala 28} 20.343 42.51 -43.993 {ca lys 29} 17.337 42.618 -41.761 {ca lys 30} 15.368 40.036 -39.765 {ca asp 31} 11.954 41.72 -39.241 {ca pro 32} 9.984 41.649 -35.986 {ca glu 33} 6.24 41.467 -35.575 @vectorlist {lp 1a} color= white master= {loops} {ca glu 33}P 6.24 41.467 -35.575 {ca gly 34} 4.898 44.616 -37.279 {ca leu 35} 7.662 45.555 -39.674 {ca phe 36} 8.751 49.184 -39.977 {ca leu 37} 11.769 50.291 -41.987 {ca gln 38} 11.551 48.51 -45.368 @vectorlist {b 2a} color=bluetint master= {beta} {ca gln 38}P 11.551 48.51 -45.368 {ca asp 39} 14.844 49.115 -47.267 {ca asn 40} 17.524 51.746 -48.019 {ca ile 41} 18.206 51.963 -44.403 {ca val 42} 21.235 54.003 -43.564 {ca ala 43} 22.257 54.773 -40.056 {ca glu 44} 24.476 57.465 -38.598 {ca phe 45} 25.702 56.625 -35.106 {ca ser 46} 27.439 59.049 -32.749 {ca val 47} 28.324 59.853 -29.154 {ca asp 48} 28.849 63.092 -27.275 {ca glu 49} 31.355 63.864 -24.575 @vectorlist {lp 2a} color= white master= {loops} {ca glu 49}P 31.355 63.864 -24.575 {ca thr 50} 29.917 62.008 -21.605 {ca gly 51} 29.988 58.678 -23.161 @vectorlist {b 3a} color=pinktint master= {beta} {ca gly 51}P 29.988 58.678 -23.161 {ca gln 52} 26.484 58.729 -24.446 {ca met 53} 25.702 57.058 -27.741 {ca ser 54} 22.872 58.133 -30.007 {ca ala 55} 21.987 57.907 -33.655 {ca thr 56} 19.746 58.734 -36.488 {ca ala 57} 18.449 56.563 -39.254 {ca lys 58} 16.578 56.738 -42.50 {ca gly 59} 14.834 54.427 -44.938 {ca arg 60} 11.663 53.529 -46.789 {ca val 61} 8.612 52.662 -44.763 {ca arg 62} 5.455 50.98 -45.93 {ca leu 63} 2.598 52.563 -44.087 {ca leu 64} -0.832 51.059 -44.023 @vectorlist {lp 3a} color= white master= {loops} {ca leu 64}P -0.832 51.059 -44.023 {ca asn 65} -2.382 50.074 -47.346 @vectorlist {b 4a} color=bluetint master= {beta} {ca asn 65}P -2.382 50.074 -47.346 {ca asn 66} 0.506 51.298 -49.505 {ca trp 67} 1.771 54.681 -48.606 {ca asp 68} 5.545 54.598 -48.457 {ca val 69} 7.524 57.365 -46.934 {ca cys 70} 11.102 58.11 -46.356 {ca ala 71} 11.251 58.174 -42.643 {ca asp 72} 14.071 59.711 -40.615 {ca met 73} 14.812 58.361 -37.195 {ca val 74} 16.259 59.222 -33.911 {ca gly 75} 17.526 56.895 -31.269 {ca thr 76} 19.262 57.556 -27.952 {ca phe 77} 21.198 54.787 -26.312 {ca thr 78} 20.827 54.197 -22.602 {ca asp 79} 23.716 52.186 -21.193 @vectorlist {lp 4a} color= white master= {loops} {ca asp 79}P 23.716 52.186 -21.193 {ca thr 80} 23.539 49.148 -18.929 {ca glu 81} 25.837 47.053 -16.829 {ca asp 82} 27.021 45.442 -19.947 {ca pro 83} 29.026 47.313 -22.499 {ca ala 84} 27.379 45.81 -25.508 @vectorlist {b 5a} color=pinktint master= {beta} {ca ala 84}P 27.379 45.81 -25.508 {ca lys 85} 23.854 46.071 -24.223 {ca phe 86} 21.874 49.221 -24.442 {ca lys 87} 18.464 50.476 -23.854 {ca met 88} 17.488 52.324 -26.978 {ca lys 89} 14.786 54.923 -26.789 {ca tyr 90} 13.74 55.909 -30.269 {ca trp 91} 11.244 58.111 -32.068 {ca gly 92} 10.898 59.661 -35.471 @vectorlist {lp 5a} color= white master= {loops} {ca gly 92}P 10.898 59.661 -35.471 {ca val 93} 10.778 63.354 -36.324 {ca ala 94} 7.146 63.26 -37.433 {ca ser 95} 5.047 62.788 -34.305 {ca phe 96} 3.048 60.24 -36.28 {ca leu 97} 5.929 57.938 -37.016 @vectorlist {b 6a} color=bluetint master= {beta} {ca leu 97}P 5.929 57.938 -37.016 {ca gln 98} 6.725 55.219 -34.486 {ca lys 99} 8.036 55.639 -31.02 {ca gly 100} 9.467 53.164 -28.52 {ca asn 101} 12.115 51.757 -26.204 {ca asp 102} 13.994 48.703 -27.402 {ca asp 103} 16.892 46.65 -26.098 {ca his 104} 19.771 47.241 -28.525 {ca trp 105} 22.724 44.949 -28.283 {ca ile 106} 25.856 44.845 -30.294 {ca val 107} 26.305 41.144 -31.007 {ca asp 108} 29.577 41.532 -32.894 {ca thr 109} 31.449 44.192 -34.888 {ca asp 110} 34.97 44.905 -36.116 @vectorlist {lp 6a} color= white master= {loops} {ca asp 110}P 34.97 44.905 -36.116 {ca tyr 111} 34.186 48.52 -36.242 {ca asp 112} 35.50 49.067 -39.717 {ca thr 113} 33.459 46.682 -41.909 {ca tyr 114} 30.503 44.966 -40.351 @vectorlist {b 7a} color=pinktint master= {beta} {ca tyr 114}P 30.503 44.966 -40.351 {ca ala 115} 28.228 44.825 -37.464 {ca val 116} 25.477 42.638 -36.231 {ca gln 117} 22.834 44.103 -34.029 {ca tyr 118} 20.146 42.182 -32.159 {ca ser 119} 16.908 43.004 -30.486 {ca cys 120} 14.371 40.971 -28.617 {ca arg 121} 11.167 42.733 -27.621 {ca leu 122} 9.312 39.839 -26.029 @vectorlist {lp 7a} color= white master= {loops} {ca leu 122}P 9.312 39.839 -26.029 {ca leu 123} 10.755 36.75 -24.394 {ca asn 124} 9.116 33.358 -24.36 {ca leu 125} 8.472 31.419 -21.146 {ca asp 126} 11.411 29.272 -22.035 {ca gly 127} 13.897 32.039 -22.336 {ca thr 128} 13.953 32.073 -26.109 {ca cys 129} 12.859 35.152 -27.943 {ca ala 130} 9.261 35.491 -28.975 @vectorlist {b 8a} color=bluetint master= {beta} {ca ala 130}P 9.261 35.491 -28.975 {ca asp 131} 9.706 38.671 -30.87 {ca ser 132} 13.063 39.74 -32.128 {ca tyr 133} 14.832 41.67 -34.859 {ca ser 134} 18.301 41.86 -36.356 {ca phe 135} 20.509 44.027 -38.471 {ca val 136} 23.612 43.067 -40.34 {ca phe 137} 25.56 46.274 -40.793 {ca ser 138} 28.022 47.227 -43.419 {ca arg 139} 30.353 50.132 -43.585 @vectorlist {lp 8a} color= white master= {loops} {ca arg 139}P 30.353 50.132 -43.585 {ca asp 140} 30.004 49.783 -47.431 {ca pro 141} 26.843 50.151 -49.528 {ca asn 142} 28.091 47.376 -51.755 {ca gly 143} 28.45 44.619 -49.268 {ca leu 144} 30.936 43.045 -46.986 {ca pro 145} 34.054 41.172 -47.805 {ca pro 146} 33.83 37.394 -48.043 {ca glu 147} 35.753 37.339 -44.812 {ca ala 148} 33.329 39.491 -42.931 {ca gln 149} 30.482 37.705 -44.572 {ca lys 150} 31.587 34.515 -42.888 {ca ile 151} 31.563 35.526 -39.261 {ca val 152} 28.364 37.407 -39.916 {ca arg 153} 26.767 34.239 -41.087 {ca gln 154} 28.285 32.481 -38.083 {ca arg 155} 26.671 35.133 -36.014 {ca gln 156} 23.219 34.888 -37.58 {ca glu 157} 23.291 31.282 -36.552 {ca glu 158} 24.188 31.847 -32.97 {ca leu 159} 21.063 33.998 -32.723 {ca cys 160} 19.077 31.151 -34.108 {ca leu 161} 17.961 33.566 -36.881 {ca ala 162} 19.93 32.258 -39.778 {ca arg 163} 18.091 32.036 -43.065 {ca gln 164} 15.435 34.232 -41.675 {ca tyr 165} 17.039 37.442 -42.672 {ca arg 166} 16.272 39.292 -45.874 {ca leu 167} 18.475 41.357 -48.136 {ca ile 168} 18.213 45.119 -47.739 {ca val 169} 18.271 47.145 -50.892 {ca his 170} 19.578 50.627 -51.392 {ca asn 171} 18.162 51.468 -54.858 {ca gly 172} 18.192 55.112 -53.888 {ca tyr 173} 14.675 55.725 -52.454 {ca cys 174} 15.524 57.93 -49.464 @subgroup dominant {labels a} @labellist {lbl} color=sea master= {labels} {C-t} 15.524 57.93 -49.464 {N-t} 23.65 21.705 -29.321 @subgroup {side ch a} @balllist {O} color= red radius= .2 {oh tyr 90} 9.709 51.116 -31.815 @balllist {S} color= yellow radius= .2 {sd met 88} 17.447 52.093 -31.157 @vectorlist {gp 1} color= sea {ca tyr 90} P 13.74 55.909 -30.269 {cb tyr 90} 13.987 54.836 -31.349 {cg tyr 90} 12.854 53.846 -31.469 {cd1 tyr 90} 12.629 52.882 -30.487 {ce1 tyr 90} 11.584 51.963 -30.588 {cz tyr 90} 10.742 52.011 -31.695 {oh tyr 90} 9.709 51.116 -31.815 {cg tyr 90} P 12.854 53.846 -31.469 {cd2 tyr 90} 11.994 53.879 -32.57 {ce2 tyr 90} 10.946 52.971 -32.687 {cz tyr 90} 10.742 52.011 -31.695 {ca phe 36} P 8.751 49.184 -39.977 {cb phe 36} 8.805 49.812 -38.576 {cg phe 36} 8.896 51.31 -38.546 {cd1 phe 36} 7.799 52.094 -38.893 {ce1 phe 36} 7.869 53.487 -38.857 {cz phe 36} 9.059 54.098 -38.459 {cg phe 36} P 8.896 51.31 -38.546 {cd2 phe 36} 10.072 51.94 -38.146 {ce2 phe 36} 10.167 53.329 -38.101 {cz phe 36} 9.059 54.098 -38.459 {ca phe 45} P 25.702 56.625 -35.106 {cb phe 45} 26.389 55.263 -34.912 {cg phe 45} 25.452 54.179 -34.47 {cd1 phe 45} 25.171 53.991 -33.117 {ce1 phe 45} 24.299 52.982 -32.706 {cz phe 45} 23.704 52.16 -33.67 {cg phe 45} P 25.452 54.179 -34.47 {cd2 phe 45} 24.856 53.353 -35.418 {ce2 phe 45} 23.978 52.342 -35.026 {cz phe 45} 23.704 52.16 -33.67 {ca phe 77} P 21.198 54.787 -26.312 {cb phe 77} 22.237 53.957 -27.077 {cg phe 77} 21.734 53.625 -28.458 {cd1 phe 77} 20.94 52.497 -28.668 {ce1 phe 77} 20.464 52.169 -29.936 {cz phe 77} 20.778 52.991 -31.015 {cg phe 77} P 21.734 53.625 -28.458 {cd2 phe 77} 22.032 54.441 -29.551 {ce2 phe 77} 21.56 54.132 -30.826 {cz phe 77} 20.778 52.991 -31.015 {ca phe 135} P 20.509 44.027 -38.471 {cb phe 135} 20.456 45.524 -38.081 {cg phe 135} 19.108 46.19 -38.316 {cd1 phe 135} 18.644 46.462 -39.608 {ce1 phe 135} 17.412 47.071 -39.837 {cz phe 135} 16.601 47.424 -38.754 {cg phe 135} P 19.108 46.19 -38.316 {cd2 phe 135} 18.283 46.558 -37.258 {ce2 phe 135} 17.038 47.167 -37.457 {cz phe 135} 16.601 47.424 -38.754 {ca phe 137} P 25.56 46.274 -40.793 {cb phe 137} 25.588 47.377 -39.717 {cg phe 137} 24.235 47.94 -39.378 {cd1 phe 137} 23.461 48.608 -40.334 {ce1 phe 137} 22.208 49.123 -40.005 {cz phe 137} 21.717 48.962 -38.705 {cg phe 137} P 24.235 47.94 -39.378 {cd2 phe 137} 23.725 47.794 -38.09 {ce2 phe 137} 22.472 48.297 -37.74 {cz phe 137} 21.717 48.962 -38.705 {ca met 88} P 17.488 52.324 -26.978 {cb met 88} 17.893 51.839 -28.392 {cg met 88} 17.577 52.841 -29.507 {sd met 88} 17.447 52.093 -31.157 {ce met 88} 15.643 52.023 -31.261 @vectorlist {gp 2} color= gold {ca leu 35} P 7.662 45.555 -39.674 {cb leu 35} 8.275 44.759 -40.846 {cg leu 35} 8.433 45.612 -42.097 {cd1 leu 35} 9.546 45.033 -42.937 {cg leu 35} P 8.433 45.612 -42.097 {cd2 leu 35} 7.152 45.62 -42.919 {ca leu 37} P 11.769 50.291 -41.987 {cb leu 37} 12.90 50.262 -40.928 {cg leu 37} 13.328 51.605 -40.33 {cd1 leu 37} 14.846 51.706 -40.39 {cg leu 37} P 13.328 51.605 -40.33 {cd2 leu 37} 12.727 52.793 -41.068 @group dominant {BRP - holo} 2animate @subgroup {ca} instance= {Calphas} @subgroup {lbl} instance= {labels} @subgroup {ret} instance= {retinol} @subgroup {side ch} @balllist {O} color= red radius= .2 {oh tyr 90} 9.642 51.266 -32.03 @balllist {S} color= yellow radius= .2 {sd met 88} 17.706 52.225 -31.229 @vectorlist {gp 1} color= sea {ca tyr 90} P 13.752 55.951 -30.291 {cb tyr 90} 13.987 54.935 -31.438 {cg tyr 90} 12.828 53.985 -31.635 {cd1 tyr 90} 12.623 52.954 -30.72 {ce1 tyr 90} 11.563 52.053 -30.853 {cz tyr 90} 10.68 52.172 -31.921 {oh tyr 90} 9.642 51.266 -32.03 {cg tyr 90} P 12.828 53.985 -31.635 {cd2 tyr 90} 11.928 54.089 -32.70 {ce2 tyr 90} 10.862 53.196 -32.85 {cz tyr 90} 10.68 52.172 -31.921 {ca phe 36} P 9.29 48.181 -39.467 {cb phe 36} 9.901 46.789 -39.259 {cg phe 36} 11.224 46.835 -38.537 {cd1 phe 36} 11.335 47.471 -37.299 {ce1 phe 36} 12.553 47.512 -36.62 {cz phe 36} 13.671 46.908 -37.196 {cg phe 36} P 11.224 46.835 -38.537 {cd2 phe 36} 12.355 46.233 -39.101 {ce2 phe 36} 13.579 46.27 -38.433 {cz phe 36} 13.671 46.908 -37.196 {ca phe 45} P 26.062 56.418 -34.911 {cb phe 45} 26.698 55.077 -34.514 {cg phe 45} 25.597 54.064 -34.443 {cd1 phe 45} 25.017 53.609 -35.625 {ce1 phe 45} 23.983 52.678 -35.602 {cz phe 45} 23.53 52.213 -34.369 {cg phe 45} P 25.597 54.064 -34.443 {cd2 phe 45} 25.128 53.596 -33.212 {ce2 phe 45} 24.092 52.662 -33.175 {cz phe 45} 23.53 52.213 -34.369 {ca phe 77} P 21.266 54.678 -26.15 {cb phe 77} 22.37 53.89 -26.86 {cg phe 77} 22.013 53.618 -28.293 {cd1 phe 77} 22.073 54.641 -29.241 {ce1 phe 77} 21.741 54.393 -30.571 {cz phe 77} 21.341 53.114 -30.951 {cg phe 77} P 22.013 53.618 -28.293 {cd2 phe 77} 21.605 52.346 -28.695 {ce2 phe 77} 21.268 52.08 -30.022 {cz phe 77} 21.341 53.114 -30.951 {ca phe 135} P 20.395 44.023 -38.479 {cb phe 135} 20.355 45.556 -38.318 {cg phe 135} 19.041 46.297 -38.529 {cd1 phe 135} 18.528 46.528 -39.804 {ce1 phe 135} 17.328 47.213 -39.986 {cz phe 135} 16.617 47.69 -38.885 {cg phe 135} P 19.041 46.297 -38.529 {cd2 phe 135} 18.315 46.79 -37.444 {ce2 phe 135} 17.114 47.477 -37.60 {cz phe 135} 16.617 47.69 -38.885 {ca phe 137} P 25.517 46.30 -40.859 {cb phe 137} 25.597 47.423 -39.818 {cg phe 137} 24.273 47.926 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forming a propeller structure. Animate to build up the propeller. Turn on "site" to see sialic acid in the active site at the top end of the propeller stucture. 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