Table I.
List of Fab-Antigen Complexes
| Number | PDB ID | Description | Resolution (Å) | R-Free |
|---|---|---|---|---|
| 1 | 1FE8 | Von Willebrand factor A3 domain/Fab fragment of IGG RU5 that inhibits collagen binding | 2.03 | 0.264 |
| 2 | 1FNS | Von Willebrand factor A1 domain I546V mutant/the function blocking Fab NMC4 | 2 | 0.207 |
| 3 | 1H0D | Human angiogenin/Fab of mAb 26-2F | 2 | 0.272 |
| 4 | 1IQD | Human factor VIII C2 domain/human monoclonal BO2C11 Fab. | 2 | 0.253 |
| 5 | 1JPS | Tissue factor/humanized Fab D3h44 | 1.85 | 0.224 |
| 6 | 1KB5 | Murine T-cell variable domain/Fab | 2.5 | 0.221 |
| 7 | 1LK3 | Engineered human interleukin-10 monomer/9D7 Fab fragment | 1.91 | 0.24 |
| 8 | 1MLC | FAB D44.1/lysozyme | 2.5 | 0.282 |
| 9 | 1OSP | Outer surface protein A of borrelia burgdorferi/Fab of a murine mAb | 1.95 | 0.295 |
| 10 | 1UJ3 | A humanized Fab fragment of anti-tissue-factor antibody/tissue factor | 2.1 | 0.227 |
| 11 | 1WEJ | IgG1 Fab fragment (of E8 antibody)/horse cytochrome C | 1.8 | 0.256 |
| 12 | 1YQV | Fab HyHEL5/lysozyme | 1.7 | 0.234 |
| 13 | 1ZTX | West Nile virus envelope protein DIII/neutralizing E16 antibody Fab | 2.5 | 0.282 |
| 14 | 2B2X | VLA1 RdeltaH I-domain/a quadruple mutant of the AQC2 Fab | 2.2 | 0.272 |
| 15 | 2CMR | HIV-1 neutralizing antibody D5 Fab/the GP41 innter-core mimetic 5-helix | 2 | 0.258 |
| 16 | 2DD8 | SARS-CoV spike receptor-binding domain/neutralizing antibody | 2.3 | 0.261 |
| 17 | 2FD6 | Human urokinase plasminogen activator/urokinase receptor and an anti-upar antibody | 1.9 | 0.276 |
| 18 | 2NXY | HIV-1 gp120 envelope glycoprotein(S334A)/CD4 and antibody 17b | 2 | 0.231 |
| 19 | 2Q8B | Malaria antigen AMA1/growth-inhibitory antibody | 2.3 | 0.256 |
| 20 | 2QQN | Neuropilin-1 b1 Domain/VEGF-blocking Fab | 2.2 | 0.207 |
| 21 | 2R0L | Short form HGFA/Inhibitory Fab75 | 2.2 | 0.248 |
| 22 | 2VDR | Integrin alphaIIBbetaA3 headpiece/a chimeric fibrinogen gamma chain peptide | 2.4 | 0.193 |
| 23 | 3D85 | Crystal structure of IL-23/neutralizing Fab | 1.9 | 0.214 |
| 24 | 3D9A | HyHel10 Fab/hen egg lysozyme | 1.2 | 0.205 |
| 25 | 1BJ1 | Vascular endothelial growth factor/neutralizing antibody | 2.4 | 0.266 |
| 26 | 1CE1 | Therapeutic antibody Fab/a synthetic peptide antigen | 1.9 | 0.27 |
| 27 | 1N8Z | Extracellular domain of human HER2/therapeutic Fab | 2.52 | 0.284 |
| 28 | 1SY6 | Crystal structure of CD3γε heterodimer/therapeutic Fab | 2.1 | 0.255 |
| 29 | 1YY9 | Extracellular domain of the epidermal growth factor receptor/neutralizing Fab | 2.61 | 0.289 |
Our study is based on analysis of 29 Fab-antigen complex crystal structures (listed above) with resolution range 1.2–2.61 Å. All the Fabs in this study are different. This dataset compares favorably with the previous studies of Fab-antigen complex crystal structure data analyses (32,35,36). For example, Jackson et al. (1999) had studied 15 Fab-antigen complexes with resolution range 1.8–3.0 Å (32). The dataset of Lo Conte et al. (1999) contained 19 Fab-antigen complexes with resolution range 1.8–3.0 Å (35). The study of MacCallum et al. (1996) was based on 26 Fab-antigen complexes with 1.8–3.1 Å (36)