Research workbench
Crystal structure of rabbit anti-HIV Fab 11A
Analyse Crystal structure of rabbit anti-HIV Fab 11A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RA7
- Type
- protein
- Length
- 864 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 11A Fab heavy chain; 11A Fab light chain
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | 11A Fab heavy chain | protein | 218 | 6% helix, 52% strand | — |
| L | 11A Fab light chain | protein | 217 | 8% helix, 51% strand | — |
| A | 11A Fab heavy chain | protein | 213 | 7% helix, 53% strand | — |
| B | 11A Fab light chain | protein | 216 | 6% helix, 52% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 395 | 0.71 | 0.82 | 35 | empty |
| 2 | 496 | 0.60 | 0.75 | 56 | 1PE |
| 3 | 446 | 0.60 | 0.75 | 47 | empty |
| 4 | 216 | 0.51 | 0.76 | 28 | empty |
| 5 | 202 | 0.47 | 0.75 | 30 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1963 Ų buried · 14 hydrogen bonds · protein-protein
- H–L · 1891 Ų buried · 15 hydrogen bonds · protein-protein
- H–A · 375 Ų buried · 8 hydrogen bonds · protein-protein
- H–B · 115 Ų buried · 0 hydrogen bonds · protein-protein
- L–A · 103 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 2 modified (disulfide, cyclization).
Compared structures
- 7RA7 · Crystal structure of rabbit anti-HIV Fab 11A · the same entry in another collection · chain H against H, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 7RA7 · PDBe 7RA7
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