Table 1. Benchmark antibody complexes.
| PDB | VL | H1 | H2 | H3 | L1 | L2 | L3 | Ag Length | Antigen | |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 1a14 | κ | H1-13-1 | H2-10-1 | H3-15 | L1-11-2 | L2-8-1 | L3-9-cis7-1 | 388 | Neuraminidase |
| 2 | 1a2y | κ | H1-13-1 | H2-9-1 | H3-10 | L1-11-2 | L2-8-1 | L3-9-cis7-2 | 129 | Lysozyme C |
| 3 | 1fe8 | κ | H1-13-1 | H2-9-1 | H3-9 | L1-11-1 | L2-8-1 | L3-9-cis7-1 | 196 | von Willebrand factor |
| 4 | 1ic7 | κ | H1-13-1 | H2-9-1 | H3-7 | L1-11-1 | L2-8-1 | L3-9-cis7-1 | 129 | Lysozyme C |
| 5 | 1iqd | κ | H1-13-1 | H2-10-1 | H3-10 | L1-12-1 | L2-8-1 | L3-9-1 | 156 | Coagulation factor VIII |
| 6 | 1n8z | κ | H1-13-1 | H2-10-1 | H3-13 | L1-11-1 | L2-8-1 | L3-9-cis7-1 | 607 | ErbB-2 |
| 7 | 1ncb | κ | H1-13-1 | H2-10-1 | H3-13 | L1-11-2 | L2-8-1 | L3-9-cis7-1 | 389 | Neuraminidase |
| 8 | 1osp | κ | H1-13-7 | H2-9-3 | H3-14 | L1-11-2 | L2-8-2 | L3-9-cis7-1 | 257 | Ozd [A |
| 9 | 1uj3 | κ | H1-13-1 | H2-10-1 | H3-10 | L1-11-2 | L2-8-1 | L3-9-cis7-1 | 205 | Tissue factor |
| 10 | 1w72 | λ | H1-13-1 | H2-10-2 | H3-15 | L1-11-3 | L2-8-1 | L3-11-1 | 274 | HLA-A1,β2-MG,peptide |
| 11 | 2adf | κ | H1-13-1 | H2-10-1 | H3-11 | L1-11-2 | L2-8-1 | L3-8-1 | 196 | von Willebrand factor |
| 12 | 2b2x | κ | H1-13-1 | H2-9-1 | H3-12 | L1-10-1 | L2-8-1 | L3-9-cis7-1 | 223 | Integrin alpha-1 |
| 13 | 2cmr | κ | H1-13-3 | H2-10-1 | H3-12 | L1-11-1 | L2-8-1 | L3-9-cis7-1 | 226 | gp41 |
| 14 | 2dd8 | λ | H1-13-10 | H2-10-1 | H3-11 | L1-11-3 | L2-8-1 | L3-10-1 | 202 | Spike glycoprotein |
| 15 | 2ghw | κ | H1-13-1 | H2-10-2 | H3-10 | L1-11-1 | L2-8-1 | L3-9-cis7-1 | 203 | Spike glycoprotein |
| 16 | 2vxt | κ | H1-13-1 | H2-10-1 | H3-6 | L1-11-1 | L2-8-1 | L3-9-cis7-1 | 157 | Interleukin-18 |
| 17 | 2xqy | κ | H1-13-1 | H2-10-1 | H3-11 | L1-15-1 | L2-8-1 | L3-9-cis7-1 | 572 | Envelope glycoprotein-H |
| 18 | 2xwt | λ | H1-13-1 | H2-10-1 | H3-12 | L1-13-1 | L2-8-2 | L3-11-1 | 239 | Thyrotropin receptor |
| 19 | 2ypv | κ | H1-13-1 | H2-10-1 | H3-12 | L1-11-2 | L2-8-1 | L3-9-cis7-1 | 253 | Lipoprotein |
| 20 | 3bn9 | κ | H1-13-1 | H2-10-2 | H3-21 | L1-11-1 | L2-8-1 | L3-9-cis7-1 | 241 | MT-SP1 |
| 21 | 3cx5 | κ | H1-14-1 | H2-9-1 | H3-15 | L1-11-2 | L2-8-1 | L3-9-cis7-1 | 185 | Rieske Iron-sulfur protein |
| 22 | 3ffd | λ | H1-13-1 | H2-10-2 | H3-11 | L1-12-3 | L2-12-2 | L3-13-1 | 108 | PTH-related |
| 23 | 3h3b | κ | H1-13-1 | H2-10-1 | H3-13 | L1-17-1 | L2-8-1 | L3-9-cis7-1 | 194 | ErbB-2 |
| 24 | 3hi6 | κ | H1-13-1 | H2-10-2 | H3-13 | L1-11-1 | L2-8-1 | L3-8-1 | 180 | Integrin alpha-L |
| 25 | 3k2u | κ | H1-13-1 | H2-10-1 | H3-11 | L1-11-1 | L2-8-1 | L3-9-cis7-1 | 257 | HGF activator |
| 26 | 3l95 | κ | H1-13-1 | H2-10-1 | H3-12 | L1-11-1 | L2-8-1 | L3-9-2 | 244 | NOTCH1 |
| 27 | 3mxw | κ | H1-13-1 | H2-10-1 | H3-12 | L1-11-1 | L2-8-1 | L3-9-cis7-1 | 169 | Sonic hedgehog protein |
| 28 | 3nid | κ | H1-13-1 | H2-10-1 | H3-12 | L1-11-2 | L2-8-1 | L3-9-cis7-1 | 457 | Integrin alpha-IIb |
| 29 | 3o2d | κ | H1-13-1 | H2-10-1 | H3-15 | L1-17-1 | L2-8-1 | L3-8-1 | 188 | CD4 |
| 30 | 3rkd | κ | H1-15-1 | H2-9-1 | H3-16 | L1-11-2 | L2-8-1 | L3-9-cis7-2 | 146 | Capsid protein |
| 31 | 3s35 | κ | H1-13-1 | H2-10-1 | H3-10 | L1-15-1 | L2-8-1 | L3-9-cis7-1 | 122 | VGFR2 |
| 32 | 3uzq | κ | H1-13-1 | H2-10-1 | H3-9 | L1-15-1 | L2-8-1 | L3-9-cis7-1 | 114 | Genome polyprotein |
| 33 | 3w9e | κ | H1-13-1 | H2-10-1 | H3-15 | L1-12-1 | L2-8-1 | L3-8-2 | 306 | Envelope glycoprotein D |
| 34 | 4cmh | κ | H1-13-1 | H2-10-1 | H3-13 | L1-11-1 | L2-8-1 | L3-9-cis7-1 | 256 | CD38 |
| 35 | 4dtg | κ | H1-13-1 | H2-10-2 | H3-14 | L1-16-1 | L2-8-1 | L3-9-cis7-1 | 66 | TFPI |
| 36 | 4dvr | κ | H1-13-1 | H2-10-1 | H3-12 | L1-11-1 | L2-8-1 | L3-8-1 | 313 | gp160 |
| 37 | 4etq | κ | H1-13-1 | H2-10-1 | H3-12 | L1-10-1 | L2-8-1 | L3-9-cis7-1 | 269 | IMV membrane protein |
| 38 | 4ffv | κ | H1-13-1 | H2-10-1 | H3-10 | L1-10-1 | L2-8-4 | L3-9-cis7-1 | 730 | Dipeptidyl peptidase 4 |
| 39 | 4fqj | λ | H1-13-1 | H2-10-1 | H3-18 | L1-13-1 | L2-8-1 | L3-11-1 | 304 | Hemagglutinin |
| 40 | 4g6j | κ | H1-13-1 | H2-10-2 | H3-11 | L1-11-1 | L2-8-1 | L3-9-cis7-1 | 158 | Interleukin-1 beta |
| 41 | 4g6m | κ | H1-15-1 | H2-9-1 | H3-12 | L1-11-2 | L2-8-1 | L3-9-cis7-1 | 150 | Interleukin-1 beta |
| 42 | 4h8w | λ | H1-13-1 | H2-10-2 | H3-12 | L1-14-2 | L2-8-1 | L3-11-1 | 353 | gp160 |
| 43 | 4ki5 | κ | H1-13-1 | H2-10-1 | H3-15 | L1-11-2 | L2-8-2 | L3-9-cis7-1 | 183 | Factor VIII |
| 44 | 4lvn | κ | H1-14-1 | H2-9-1 | H3-13 | L1-12-1 | L2-8-1 | L3-9-cis7-1 | 344 | Subtilisin-like SP |
| 45 | 4ot1 | λ | H1-13-1 | H2-10-1 | H3-24 | L1-13-1 | L2-8-2 | L3-10-1 | 129 | Envelope glycoprotein B |
| 46 | 4qci | λ | H1-13-1 | H2-10-2 | H3-13 | L1-11-3 | L2-8-1 | L3-9-2 | 110 | PDGFR Beta |
| 47 | 4xnq | λ | H1-14-1 | H2-9-1 | H3-16 | L1-11-3 | L2-8-1 | L3-9-1 | 212 | Hemagglutinin (Fragment) |
| 48 | 4ydk | κ | H1-13-1 | H2-10-2 | H3-22 | L1-11-1 | L2-8-1 | L3-9-2 | 353 | gp160 |
| 49 | 5b8c | κ | H1-13-1 | H2-10-1 | H3-13 | L1-15-1 | L2-8-1 | L3-9-cis7-1 | 139 | PD1 |
| 50 | 5bv7 | λ | H1-13-1 | H2-10-2 | H3-19 | L1-11-3 | L2-8-1 | L3-10-1 | 422 | PC-sterol acyltransferase |
| 51 | 5d93 | κ | H1-13-1 | H2-10-1 | H3-9 | L1-10-1 | L2-8-1 | L3-9-cis7-1 | 244 | Sulfhydryl oxidase 1 |
| 52 | 5d96 | κ | H1-13-1 | H2-9-1 | H3-12 | L1-11-1 | L2-8-1 | L3-9-cis7-1 | 244 | Sulfhydryl oxidase 1 |
| 53 | 5en2 | κ | H1-13-1 | H2-10-1 | H3-17 | L1-11-1 | L2-8-1 | L3-9-cis7-1 | 141 | Pre-glycoprotein GP |
| 54 | 5f9o | κ | H1-13-1 | H2-10-1 | H3-15 | L1-11-1 | L2-8-1 | L3-8-1 | 352 | gp120 core |
| 55 | 5ggs | κ | H1-13-3 | H2-10-1 | H3-13 | L1-15-1 | L2-8-1 | L3-9-cis7-1 | 123 | PD1 |
| 56 | 5hi4 | λ | H1-13-1 | H2-10-2 | H3-11 | L1-13-2 | L2-8-1 | L3-9-1 | 132 | Interleukin-17A homodimer |
| 57 | 5j13 | λ | H1-13-1 | H2-10-2 | H3-15 | L1-11-3 | L2-8-2 | L3-11-1 | 147 | Thymic stromal lymphopoietin |
| 58 | 5l6y | λ | H1-13-1 | H2-10-1 | H3-15 | L1-11-3 | L2-8-1 | L3-11-1 | 112 | Interleukin-13 |
| 59 | 5mes | λ | H1-13-1 | H2-10-2 | H3-12 | L1-13-1 | L2-8-1 | L3-11-1 | 162 | Mcl-1 homolog |
| 60 | 5nuz | κ | H1-13-1 | H2-10-1 | H3-13 | L1-15-1 | L2-8-1 | L3-9-cis7-1 | 156 | Pre-glycoprotein GP |
For each CDR, the PyIgClassify cluster is given. For H3, only the length is given. VL provides the kappa or lambda identify of the light chain variable domain of the antibody. Antibodies to the same antigen bind in different locations and are not the same antibody.