@text
Kinemage Supplement to Branden & Tooze "Introduction to Protein Structure", Second Edition
Chapter 15 -  RECOGNITION OF FOREIGN MOLECULES BY THE IMMUNE SYSTEM

		Contents of file c15Immun.kin:
*{Kin 1}* Immunoglobulin domains - CL, VL, light chain & FAB (Fig. 15.7-15.11)
*{Kin 2}* Intact IgG molecules, Y-shaped vs T-shaped (Fig. 15.17)
*{Kin 3}* Lysozyme/antibody complex - overview & spec. binding (Fig. 15.15-16)
*{Kin 4}* HLA-A2, an MHC class II antigen, with bound peptide (Fig. 15.18-20)
*{Kin 5}* T-cell receptor, complexed with MHC class I (Fig. 15.22-23)
*{Kin 6}* Multiple fibronectin domains (Fig. 15.24)
*{Kin 7}* Two domains of CD4, with beta ribbons (Fig. 15.25)

    *{Kinemage 1}* is an animated tour of the domain organization for the Fab part of an immunoglobulin, and the internal organization of those domains.  The start-up frame is a constant domain (CL), colored as in Fig. 15.8a, with the rear beta sheet in skyblue and the front sheet in seagreen; the strands are all antiparallel and have a Greek key topology.  The highly-conserved disulfide bond that crosses the inside of the barrel is in yellow.  The connection in pink is homologous to the region that is enlarged to form CDR2 (Complementarity-Determining Region 2) in variable domains.  Animate to continue the tour, next with a view of the interface between the CL domain and the CH1 domain (gray), which is packed against the skyblue sheet.
    Next (animate) is a similar view of a variable domain (VL); the blue and green beta strands are in equivalent positions and have equivalent connections as in the constant domain.  The pink region of CDR2 is longer and has two additional short strands.  Along with the CDR1 and CDR3 loops and the 3 CDRs on VH, it makes up the hypervariable region that changes sequence and conformation in various antibody molecules to provide complementary binding for an extremely wide variety of antigens.  We then view VL from the edge of the beta sandwich, showing VH (gray) forming a beta-barrel with the seagreen sheet this time.
    Then both domains of the light chain are shown, which are joined by a somewhat flexible linker.  Then the heavy chain is added to see all 4 domains of this Fab fragment.  The two variable domains associate tightly, with their green sheets back-to-back and their CDRs close together, and the two constant domains associate tightly with their two blue sheets back-to-back.  In an intact IgG, the second half of the heavy chains from two Fabs associate to form a 4-domain FC region made up of CH2 and CH3 domains.  Next there is a view of VL and VH from the top end, which makes up the antigen-combining region.  Last, the CDRs of the variable domains of both chains are shown.

    [To see the limited range of different conformations for a CDR, refer to Kin. 1 of c17Engin.kin.]  

    *{Kinemage 2}* shows the structure of an intact IgG-type immunoglobulin, including the Fc (bottom), both Fab portions (top arms), and the hinge region that joins them.  Light chains are in cyan and skyblue, heavy chains are in purple and magenta, and the local 2-fold axes within each Fab or Fc part are in pinktint.  The overall structure is T-shaped but somewhat asymmetrical (as in Fig. 15.17).  Animate, to change between two crystal structures of closely-related IgGs, to see some of the great flexibility possible for the hinge conformation and the overall shape.  The second example is more classically Y-shaped (as in the diagrams of Fig. 15.2), with the Fab and Fc parts closer together and angled differently.
    Make sure that the animation state is showing the original IgG T and choose View2 for a closeup of the Fc portion.  The CH2 domains of Fc make no direct contacts with each other but have two copies of a branched carbohydrate between them (shown in white), attached to heavy-chain Asn 314 (greentint).  View3 is a closeup of the hinge region, which contains a lot of Pro and Gly to promote staying extended and flexible, and which has the two chains joined by 3 closely-spaced disulfides (green).  
    View4 shows one of the Fab regions, which look very much the same as the isolated Fab we saw in Kin.1.  Turn on "CDRs" to highlight the 3 hypervariable loops from each chain that contribute to the antigen-binding site.  Choose View5 for a closeup of that site from the antigen's point of view.  Then recapitulate animation of the overall conformational changes in views 1 or 7, or explore the somewhat different CH2 and hinge structures of the Y-shaped version in views 8 and 9.

    *{Kinemage 3}* shows a complex of the enzyme lysozyme with an anti-lysozyme antibody (the Fab portion of Hy/Hel-10).  Lysozyme is in greentint, and the Fab in white and yellowtint, with yellow SS bridges.  This is a different anti-lysozyme antibody than the one illustrated in Fig. 15.15 and 15.16, and it binds to a completely separate region on lysozyme (Gln 121 from the other interface is shown in blue for comparison, off to the side), but the general nature of the binding is quite similar.  As can be seen in View2, the interface is quite extensive and fairly flat, and lysozyme sits over almost all of the surface made by the tops of the two variable domains.  In addition to direct protein-protein contacts, there is a good deal of buried water in the interface.  This particular complex buries and complements a pair of charged residues, in addition to the usual aromatic, hydrophobic, and H-bond interactions.  Choose View3 and turn on "binding sc" to see the set of heavy-chain side chains that bind Lys 97 of lysozyme.  The lysine is sandwiched between two aromatic rings and makes a charged H-bond to Asp 32, which in turn is H-bonded to an Asn.

    *{Kinemage 4}* shows the Calpha backbone of the HLA-A2 molecule, a class II major histocompatibility complex (MHC) antigen involved in T-cell activation.  It consists of 2 chains, one alpha1-alpha2 (greens) and one beta1-beta2 (yellows).  Alpha2 and beta2 are related to immunoglobulin constant domains, and are paired at bottom of the molecule (in View1, like Fig. 15.18a), near the cell surface.  A1 and b1 are the similar halves of the antigen-presenting top portion, which consists of a "floor" of an 8-stranded antiparallel beta sheet with two long alpha-helices on top separated by a crevice in which the antigen peptide binds (shown in blues).  Each of a1 and a2 has a simple topology of 4 up&down beta strands (called a "W") followed by a long helix across the top of the sheet.  MHC proteins are highly polymorphic, with the different classes binding different sets of peptides that have been cleaved from foreign antigenic proteins.  Choose View2 and turn on "side ch" to see more detail of the peptide binding, as in Fig. 15.20d.  The peptide backbone is extended, in a polyproline II type conformation.

    *{Kinemage 5}* shows the complex of T-cell receptor and an MHC class I antigen with bound peptide.  The MHC class I molecule has a different domain organization than class II, with both halves of the antigen-presenting portion in one 3-domain chain and a separate chain with the single b2m immunoglobulin-like domain.  The peptide (in gold), as typical for class I, is shorter and with a less regular conformation than those that bind to class II MHC.  The two termini of the peptide are bound within the MHC cleft, while the middle portion bulges up toward the T-cell receptor.  View1 shows the T-cell receptor portion of this complex, which has both of the variable domains (pinks) but only one of the two constant domains (blue).  View2 shows the entire complex, from a view like Fig. 15.23.

    *{Kinemage 6}* shows repeats 7 through 10 of the cell-surface protein fibronectin, each with a fibronectin III domain structure quite similar to an immunoglobulin domain.  The bottom domain has a loop with the RGD sequence that is implicated in binding to other cells.  The domains differ slightly in sequence and in structure details, and the spatial relationship between successive domains is different for each of these pairs.  View2 is a close-up of the RGD domain, colored as in Fig. 15.24, with the rear 3-strand beta sheet in orange and the front 4-strand sheet in green.

    *{Kinemage 7}* is a ribbon schematic of the first two domains of the T-cell surface co-receptor CD4, colored and oriented to match Fig. 15.25.  Each domain is immunoglobulin-like, as seen in View2 and View3, but in the second (green) domain the disulfide is a "staple" between two adjacent beta strands rather than the usual bridge between the two sides of the beta sandwich.  In View1 it can be seen that the connection between the two domains is a single, continuous beta strand (it has H-bonds in both directions from a single peptide in the middle), which can help rigidify the shape of the overall structure.


    Kinemages 2 and 7 were made by Claudia J. Richardson.

    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.
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@caption (B&T Fig. 15.8, 15.9)
Immunoglobulin domains - CL constant domain (View1) and VL variable domain (View2), with rear beta sheet in skyblue, front beta sheet in seagreen, disulfide in yellow, and CDR loops or homologous region in pink.  Animate for a tour of the parts of the Fab fragment.  (from PDB file 2FB4)
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{ca gly l 67}P 53.740 54.692 54.922
{ca ala l 68}50.600 56.075 53.414
{ca gly l 76}P 65.365 72.931 39.915
{ca leu l 77}62.035 74.218 38.690
{ca gln l 78}62.110 75.162 34.983
{ca ser l 79}59.472 76.950 32.806
{ca glu l 80}58.496 73.632 31.170
{ca asp l 81}57.361 72.351 34.534
{ca glu l 82}54.243 74.446 34.566
{ca thr l 106}P 53.277 77.806 38.611
{ca val l 107}56.751 79.112 37.800
{ca leu l 108}56.772 82.265 39.797
{ca gly l 109}57.552 85.677 38.525
@vectorlist {sheet 1} color= sky master= {sheet 1}
{arrow}P 46.999 64.627 48.413
{ca gln l 6}47.173 66.484 46.748
{arrow}44.825 65.631 46.836
{"}P 48.739 59.490 51.446
{ca gly l 24}46.574 58.321 51.001
{arrow}46.322 60.774 50.591
{"}P 54.859 56.791 54.154
{ca gly l 67}53.740 54.692 54.922
{arrow}55.833 54.137 53.673
{"}P 64.668 71.889 42.078
{ca gly l 76}65.365 72.931 39.915
{arrow}65.440 70.439 39.727
{ca leu l 4}P 44.265 60.491 46.942
{ca thr l 5}44.828 63.965 48.378
{ca gln l 6}47.173 66.484 46.748
{ca gln l 16}P 64.161 76.303 43.245
{ca arg l 17}63.286 72.907 44.609
{ca val l 18}59.545 72.311 44.526
{ca thr l 19}57.942 69.203 45.960
{ca ile l 20}54.380 67.887 45.744
{ca ser l 21}52.762 65.671 48.366
{ca cys l 22}50.102 62.935 47.960
{ca ser l 23}48.337 61.660 51.033
{ca gly l 24}46.574 58.321 51.001
{ca arg l 60}P 65.472 66.447 38.215
{ca phe l 61}62.320 64.465 38.908
{ca ser l 62}62.467 62.135 41.857
{ca gly l 63}59.907 60.139 43.777
{ca ser l 64}59.586 59.028 47.335
{ca lys l 65}57.154 56.947 49.397
{ca ser l 66}56.687 56.109 53.072
{ca gly l 67}53.740 54.692 54.922
{ca ala l 68}P 50.600 56.075 53.414
{ca ser l 69}52.268 59.119 51.929
{ca ala l 70}54.271 59.847 48.805
{ca ser l 71}55.920 62.802 47.219
{ca leu l 72}57.232 64.110 43.904
{ca ala l 73}60.395 66.320 43.912
{ca ile l 74}61.267 68.773 41.133
{ca gly l 75}64.798 69.707 41.717
{ca gly l 76}65.365 72.931 39.915
@vectorlist {sheet 2} color= sea master= {sheet 2}
{arw}P 49.452, 67.281, 30.221
{ca leu l 38} 48.318, 69.505, 30.359
{arw} 48.394, 68.443, 32.621
{arw}P 45.864, 49.836, 45.318
{ca asp l 91} 43.578, 50.231, 46.249
{arw} 43.724, 51.142, 43.925
{arrow}P 53.827 75.085 42.557
{ca ser l 11}54.830 77.265 43.260
{arrow}53.472 76.307 45.127
{arw}P 52.737 76.198 40.448
{ca thr l 106}53.277 77.806 38.611
{arrow}52.983 75.506 37.676
{ca ser l 9}P 48.917 74.177 43.910
{ca ala l 10}52.649 74.367 44.336
{ca ser l 11}54.830 77.265 43.260
{ca val l 32}P 52.723 55.049 43.494
{ca asn l 33}52.969 56.525 39.990
{ca trp l 34}53.170 60.216 39.059
{ca tyr l 35}51.761 61.740 35.870
{ca gln l 36}52.348 65.079 34.278
{ca gln l 37}49.433 66.479 32.315
{ca leu l 38}48.318 69.505 30.359
{ca pro l 39}44.528 69.703 30.977
{ca glu l 82}P 54.243 74.446 34.566
{ca thr l 83}51.614 71.736 34.353
{ca asp l 84}49.248 69.531 36.327
{ca tyr l 85}50.642 66.604 38.305
{ca tyr l 86}48.730 63.522 39.506
{ca cys l 87}49.816 60.717 41.799
{ca ala l 88}48.126 57.312 41.462
{ca ala l 89}47.838 53.896 43.136
{ca trp l 90}45.811 50.705 43.260
{ca asp l 91}43.578 50.231 46.249
{ca ala l 96}P 40.213 50.208 42.086
{ca tyr l 97}42.882 52.365 40.550
{ca val l 98}42.836 55.687 42.378
{ca phe l 99}44.004 59.101 41.119
{ca gly l 100}45.141 61.984 43.241
{ca thr l 101}43.064 65.213 43.165
{ca gly l 102}46.005 66.821 41.425
{ca thr l 103}48.382 69.784 41.690
{ca lys l 104}49.003 72.766 39.490
{ca val l 105}52.511 74.221 39.438
{ca thr l 106}53.277 77.806 38.611
@vectorlist {CDR} color= pink master= {CDR's}
{arrow}P 57.920 53.057 39.204
{ca arg l 49}56.722 52.175 41.213
{arrow}55.298 53.861 40.039
{"}P 60.113 56.994 34.535
{ca pro l 54}61.070 56.090 32.410
{arrow}62.832 56.152 34.183
{ca gly l 24}P 46.574 58.321 51.001
{ca thr l 25}45.456 55.464 53.274
{ca ser l 26}46.619 52.026 54.343
{ca ser l 27}44.668 50.387 51.572
{ca asn l 27a}46.246 52.226 48.627
{ca ile l 27b}49.615 54.004 49.172
{ca gly l 28}50.148 51.989 52.327
{ca ser l 29}49.700 48.784 50.339
{ca ser l 30}50.763 49.429 46.763
{ca thr l 31}53.309 51.447 44.673
{ca val l 32}52.723 55.049 43.494
{ca met l 41}P 45.415 66.316 26.876
{ca ala l 42}47.027 62.898 27.343
{ca pro l 43}49.024 62.529 30.542
{ca lys l 44}52.536 61.174 30.515
{ca leu l 45}54.109 58.794 33.091
{ca leu l 46}56.874 60.612 35.012
{ca ile l 47}57.516 58.212 37.890
{ca tyr l 48}56.514 54.539 38.283
{ca arg l 49}56.722 52.175 41.213
{ca asp l 50}57.395 54.942 43.805
{ca ala l 51}60.766 56.057 42.565
{ca met l 52}61.536 54.793 39.097
{ca arg l 53}61.818 56.987 36.031
{ca pro l 54}61.070 56.090 32.410
{ca asp l 91}P 43.578 50.231 46.249
{ca val l 92}43.607 46.525 47.329
{ca ser l 93}40.332 46.769 49.429
{ca leu l 94}38.248 48.598 46.767
{ca asn l 95}39.840 46.879 43.833
{ca ala l 96}40.213 50.208 42.086
@balllist {S} color= gold radius= 0.25 master= {SS}
{sg cys l 22}49.578 60.677 46.251
{sg cys l 87}48.929 61.216 44.430
@vectorlist {ss} color= yellow master= {SS}
{ca cys l 22}P 50.102 62.935 47.960
{cb cys l 22}50.634 62.048 46.799
{sg cys l 22}49.578 60.677 46.251
{sg cys l 87}48.929 61.216 44.430
{cb cys l 87}50.236 60.750 43.279
{ca cys l 87}49.816 60.717 41.799
@labellist {CDR lbl} color= hotpink master= {labels}
{ CDR L1}49.700 48.784 50.339
{ CDR L3}40.332 46.769 49.429
{CDR L2}54.762 52.601 41.812
@labellist {N lbl} color= blue master= {labels}
{ N}37.580 54.759 49.388

@group {VL-CL} dominant animate moview= 4
@subgroup {VL } instance= {VL}
@subgroup {VH} dominant
@vectorlist {ca-ca} color= gray
{ca glu h 1}P 56.019 52.320 19.417
{ca val h 2}52.829 51.682 21.334
{ca gln h 3}49.937 53.678 19.865
{ca leu h 4}46.423 53.884 21.416
{ca val h 5}43.663 55.651 19.383
{ca gln h 6}40.229 56.300 20.973
{ca ser h 7}37.071 56.651 18.917
{ca gly h 8}33.299 56.871 19.290
{ca gly h 9}32.792 59.983 21.378
{ca gly h 10}29.790 62.217 20.931
{ca val h 11}27.046 64.490 22.226
{ca val h 12}23.982 62.769 23.689
{ca gln h 13}21.061 63.460 25.959
{ca pro h 14}20.542 61.831 29.403
{ca gly h 15}19.610 58.182 29.434
{ca arg h 16}21.092 57.466 25.998
{ca ser h 17}24.060 55.271 24.976
{ca leu h 18}27.489 55.368 23.403
{ca arg h 19}30.240 52.915 22.606
{ca leu h 20}33.894 53.843 22.693
{ca ser h 21}36.662 51.922 21.017
{ca cys h 22}40.425 51.969 21.474
{ca ser h 23}42.472 50.509 18.715
{ca ser h 24}46.069 49.583 19.390
{ca ser h 25}49.396 48.791 17.660
{ca gly h 26}53.126 48.422 18.528
{ca phe h 27}52.679 45.712 21.225
{ca ile h 28}51.274 42.245 21.969
{ca phe h 29}47.887 43.485 22.996
{ca ser h 30}46.699 40.279 24.657
{ca ser h 31}49.491 40.487 27.261
{ca tyr h 32}48.475 43.592 29.080
{ca ala h 33}45.609 44.871 31.201
{ca met h 34}43.856 47.903 29.661
{ca tyr h 35}42.253 50.955 31.311
{ca trp h 36}39.591 53.567 30.687
{ca val h 37}40.149 56.926 32.458
{ca arg h 38}38.121 60.087 32.052
{ca gln h 39}38.486 63.811 32.652
{ca ala h 40}35.549 66.164 33.234
{ca pro h 41}36.158 69.693 32.052
{ca gly h 42}38.040 71.602 34.693
{ca lys h 43}38.445 68.543 36.869
{ca gly h 44}41.063 65.859 37.531
{ca leu h 45}41.710 62.336 36.191
{ca glu h 46}39.083 59.765 37.241
{ca trp h 47}39.661 56.013 36.639
{ca val h 48}36.679 54.250 35.015
{ca ala h 49}37.595 50.605 34.493
{ca ile h 50}40.257 47.938 34.044
{ca ile h 51}40.139 44.631 32.195
{ca trp h 52}42.637 41.764 32.532
{ca asp h 53}44.835 40.582 29.672
{ca asp h 54}42.526 37.625 28.876
{ca gly h 55}39.352 39.508 29.863
{ca ser h 56}38.690 37.021 32.642
{ca asp h 57}37.838 39.785 35.038
{ca gln h 58}36.969 43.465 34.954
{ca his h 59}36.670 46.144 37.675
{ca tyr h 60}34.738 49.419 37.679
{ca ala h 61}34.542 52.777 39.469
{ca asp h 62}31.523 52.877 41.826
{ca ser h 63}29.909 55.742 39.821
{ca val h 64}29.746 53.643 36.695
{ca lys h 65}29.146 50.113 37.813
{ca gly h 66}26.258 48.550 35.983
{ca arg h 67}25.926 51.279 33.347
{ca phe h 68}29.343 50.742 31.723
{ca thr h 69}30.845 47.535 30.300
{ca ile h 70}34.528 47.105 29.476
{ca ser h 71}35.409 44.358 27.064
{ca arg h 72}38.150 43.548 24.595
{ca asn h 73}38.884 41.714 21.409
{ca asp h 74}42.440 40.340 21.515
{ca ser h 75}41.881 39.122 18.025
{ca lys h 76}41.444 42.617 16.725
{ca asn h 77}43.668 44.344 19.348
{ca thr h 78}40.685 46.598 20.396
{ca leu h 79}39.261 47.738 23.688
{ca phe h 80}35.582 48.744 24.067
{ca leu h 81}33.557 50.814 26.498
{ca gln h 82}29.753 50.335 26.286
{ca met h 83}28.206 53.265 28.057
{ca asp h 84}24.536 52.876 28.908
{ca ser h 85}22.036 55.220 30.625
{ca leu h 86}24.462 58.089 30.416
{ca arg h 87}24.288 60.954 32.925
{ca pro h 88}25.416 64.593 32.599
{ca glu h 89}28.112 63.852 35.157
{ca asp h 90}29.637 61.456 32.686
{ca thr h 91}30.711 64.330 30.478
{ca gly h 92}34.470 64.233 29.926
{ca val h 93}37.405 63.267 27.748
{ca tyr h 94}37.859 59.482 27.723
{ca phe h 95}41.328 57.967 27.545
{ca cys h 96}42.348 54.401 27.154
{ca ala h 97}45.663 53.336 28.625
{ca arg h 98}47.863 50.264 28.784
{ca asp h 99}48.771 48.695 32.133
{ca gly h 100}52.535 48.363 32.093
{ca gly h 101}52.741 45.159 34.136
{ca his h 101a}51.857 41.510 33.918
{ca gly h 101b}48.263 41.482 32.772
{ca phe h 101c}46.471 42.413 36.028
{ca cys h 101d}46.541 44.362 39.285
{ca ser h 102}46.349 42.814 42.743
{ca ser h 103}47.516 42.965 46.364
{ca ala h 104}50.798 41.646 44.994
{ca ser h 104a}51.424 44.180 42.274
{ca cys h 104b}49.988 46.964 40.061
{ca phe h 104c}52.173 48.754 37.579
{ca gly h 104d}49.554 51.259 36.480
{ca pro h 105}48.936 53.132 33.198
{ca asp h 106}52.054 53.458 31.128
{ca tyr h 107}51.073 54.558 27.702
{ca trp h 108}47.928 56.625 27.071
{ca gly h 109}45.774 57.446 24.050
{ca gln h 110}44.743 60.926 22.909
{ca gly h 111}41.198 61.044 24.311
{ca thr h 112}37.712 61.029 22.852
{ca pro h 113}35.231 63.650 24.220
{ca val h 114}31.828 62.722 25.609
{ca thr h 115}29.145 65.343 26.230
{ca val h 116}25.906 64.409 28.010
{ca ser h 117}23.496 67.320 28.356
{ca ser h 118}19.828 68.098 28.821
@vectorlist {ss} color= gold master= {SS}
{ca cys h 22}P 40.425 51.969 21.474
{cb cys h 22}40.847 51.978 22.951
{sg cys h 22}42.611 52.068 23.299
{sg cys h 96}42.880 53.671 24.547
{cb cys h 96}42.051 53.329 26.084
{ca cys h 96}42.348 54.401 27.154
{ca cys h 101d}P 46.541 44.362 39.285
{cb cys h 101d}45.967 45.786 39.249
{sg cys h 101d}46.915 46.919 38.202
{sg cys h 104b}47.582 48.410 39.462
{cb cys h 104b}48.727 47.641 40.639
{ca cys h 104b}49.988 46.964 40.061

@group {Light ch} dominant animate moview= 6
@subgroup {VL } instance= {VL}
@subgroup {CL } instance= {CL}

@group {Fab} dominant animate moview= 6
@subgroup {VL } instance= {VL}
@subgroup {CL } instance= {CL}
@subgroup {VH } instance= {VH}
@subgroup {CH1 } instance= {CH1}

@group {VL-VH top} dominant animate moview= 5
@subgroup {VL } instance= {VL}
@subgroup {VH } instance= {VH}

@group {ant-comb} dominant animate moview= 5
@subgroup {VL } instance= {VL}
@subgroup {VH } instance= {VH}
@subgroup {CDR's} dominant
@labellist {lbl} color= pink master= {labels}
{ CDR H1}   49.491, 40.487, 27.261
{   CDR H2}   37.838, 39.785, 35.038
{     CDR H3}   46.541, 44.362, 39.285
@vectorlist {ca-ca} color= pinktint master= {CDR's}
{ca ser h 25}P 49.396 48.791 17.660
{ca gly h 26}53.126 48.422 18.528
{ca phe h 27}52.679 45.712 21.225
{ca ile h 28}51.274 42.245 21.969
{ca phe h 29}47.887 43.485 22.996
{ca ser h 30}46.699 40.279 24.657
{ca ser h 31}49.491 40.487 27.261
{ca tyr h 32}48.475 43.592 29.080
{ca ala h 33}45.609 44.871 31.201
{ca trp h 52}P 42.637 41.764 32.532
{ca asp h 53}44.835 40.582 29.672
{ca asp h 54}42.526 37.625 28.876
{ca gly h 55}39.352 39.508 29.863
{ca ser h 56}38.690 37.021 32.642
{ca asp h 57}37.838 39.785 35.038
{ca gln h 58}36.969 43.465 34.954
{ca his h 59}36.670 46.144 37.675
{ca arg h 98}P 47.863 50.264 28.784
{ca asp h 99}48.771 48.695 32.133
{ca gly h 100}52.535 48.363 32.093
{ca gly h 101}52.741 45.159 34.136
{ca his h 101a}51.857 41.510 33.918
{ca gly h 101b}48.263 41.482 32.772
{ca phe h 101c}46.471 42.413 36.028
{ca cys h 101d}46.541 44.362 39.285
{ca ser h 102}46.349 42.814 42.743
{ca ser h 103}47.516 42.965 46.364
{ca ala h 104}50.798 41.646 44.994
{ca ser h 104a}51.424 44.180 42.274
{ca cys h 104b}49.988 46.964 40.061
{ca phe h 104c}52.173 48.754 37.579
{ca gly h 104d}49.554 51.259 36.480
{ca pro h 105}48.936 53.132 33.198
{ca asp h 106}52.054 53.458 31.128

@kinemage 2
@caption (B&T Fig. 15.17, 15.2)
The Calpha backbone for an intact IgG-type immunoglobulin molecule.  The light chains are in cyan and skyblue, the heavy chains in purple and magenta, and the bound carbohydrate in Fc in white.  Animate to switch between the structures of two related IgGs, to see the relative motion of the parts.
(from PDB files 1IGY, 1IGT)
@onewidth
@viewid {overview}
@zoom 1.05 
@zslab 200
@center -2.679 -23.21 1.434
@matrix
-0.19224 -.54751 .81442 .9274 .17002 .33321 -.3209 .81934 .47507
@2viewid {Fc  T}
@2zoom 2.22
@2zslab 160
@2center 16.182 -12.896 -24.888
@2matrix
-0.544263 -.805696 -.233732 -.579599 .15971 .799097 -.6065 .57039 -.553906
@3viewid {hinge SSs  T}
@3zoom 3.83
@3zslab 150
@3center 6.098 -11.396 14.511
@3matrix
-0.223359 -.389714 .89344 .965881 .034778 .256639 -.131087 .92028 .368649
@4viewid {Fab}
@4zoom 2.47
@4zslab 200
@4center 3.149 -55.332 45.374
@4matrix
-0.656322 .461103 .59718 -.217658 -.873576 .435303 .722403 .155717 .67371
@5viewid {antigen site}
@5zoom 2.96 
@5zslab 80
@5center 8.235 -78.989 55.647
@5matrix
0.45348 -.85115 .26437 .50432 .00048 -.86352 .73486 .52492 .42947
@7viewid {overview 2}
@7zoom 1.05
@7zslab 200
@7center -2.411 -16.932 8.823
@7matrix
-0.147857 -.836351 .527878 .988593 -.109506 .103404 -.028676 .537146 .843
@8viewid {Fc  Y}
@8zoom 2.22
@8zslab 120
@8center 27.690 -14.247 -20.346
@8matrix
-0.08367 .304603 .948797 .830985 .546812 -.10227 -.549966 .779881 -.29887
@9viewid {hinge SSs  Y}
@9zoom 3.83
@9zslab 140
@9center 25.082 -14.619 6.81
@9matrix
0.08479 -.619445 .780448 .99377 .109438 -.021107 -.072335 .777374 .624864
@master {SS}
@master {axes}
@master {CDRs}
@group {IgG  T} animate
@subgroup {light ch 1} dominant
@vectorlist {Calphas} color= cyan
{ ca  asp a 1 }P 1.649 -84.304 45.569
{ ca  ile a 2 }-0.861 -83.420 48.270
{ ca  val a 3 }-2.524 -80.212 47.174
{ ca  leu a 4 }-3.913 -78.072 49.981
{ ca  thr a 5 }-7.110 -75.985 49.474
{ ca  gln a 6 }-7.379 -72.842 51.537
{ ca  ser a 7 }-10.771 -71.152 51.476
{ ca  pro a 8 }-12.014 -68.592 50.934
{ ca  ser a 9 }-9.551 -66.586 48.873
{ ca  ser a 10 }-10.179 -63.201 50.522
{ ca  leu a 11 }-12.273 -61.884 53.386
{ ca  ser a 12 }-13.426 -58.624 54.907
{ ca  ala a 13 }-14.773 -58.129 58.413
{ ca  ser a 14 }-15.005 -55.478 61.108
{ ca  leu a 15 }-12.507 -55.005 63.925
{ ca  gly a 16 }-13.047 -57.288 66.902
{ ca  asp a 17 }-14.821 -59.840 64.743
{ ca  thr a 18 }-13.921 -63.492 65.023
{ ca  ile a 19 }-13.192 -65.039 61.610
{ ca  thr a 20 }-12.414 -68.555 60.368
{ ca  ile a 21 }-10.068 -69.462 57.531
{ ca  thr a 22 }-9.855 -73.098 56.465
{ ca  cys a 23 }-7.613 -75.563 54.636
{ ca  his a 24 }-8.274 -78.981 53.190
{ ca  ala a 25 }-6.024 -81.655 51.933
{ ca  ser a 26 }-6.230 -84.300 49.274
{ ca  gln a 27 }-4.451 -87.020 51.273
{ ca  asn a 28 }-4.451 -87.331 55.094
{ ca  ile a 29 }-1.718 -85.208 56.766
{ ca  asn a 30 }-2.500 -86.160 60.343
{ ca  val a 31 }-1.722 -82.968 62.169
{ ca  trp a 32 }1.213 -81.650 60.179
{ ca  leu a 33 }-0.135 -78.217 59.268
{ ca  ser a 34 }1.445 -74.833 59.704
{ ca  trp a 35 }-0.072 -71.362 59.368
{ ca  tyr a 36 }1.855 -68.332 58.178
{ ca  gln a 37 }1.079 -64.632 58.173
{ ca  gln a 38 }2.409 -62.261 55.490
{ ca  lys a 39 }1.515 -58.601 56.044
{ ca  pro a 40 }1.833 -56.677 52.720
{ ca  gly a 41 }5.520 -56.148 52.146
{ ca  asn a 42 }7.106 -57.842 55.184
{ ca  ile a 43 }8.168 -61.533 55.184
{ ca  pro a 44 }5.997 -64.415 56.392
{ ca  lys a 45 }6.237 -65.274 60.045
{ ca  leu a 46 }5.271 -68.632 61.488
{ ca  leu a 47 }1.964 -68.470 63.372
{ ca  ile a 48 }1.050 -72.075 64.171
{ ca  tyr a 49 }2.580 -75.491 63.772
{ ca  lys a 50 }1.289 -78.969 64.554
{ ca  ala a 51 }-2.254 -77.805 63.774
{ ca  ser a 52 }-2.909 -76.063 67.082
{ ca  asn a 53 }0.527 -75.316 68.441
{ ca  leu a 54 }0.881 -71.566 68.651
{ ca  his a 55 }4.327 -70.167 67.887
{ ca  thr a 56 }6.147 -67.669 70.097
{ ca  gly a 57 }4.628 -64.189 70.074
{ ca  val a 58 }1.251 -65.172 68.620
{ ca  pro a 59 }-1.230 -63.422 70.950
{ ca  ser a 60 }-3.838 -65.857 72.307
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