Research workbench
Crystal structure analysis of anti-HIV-1 Fab 447-52D in complex with V3 peptide
Analyse Crystal structure analysis of anti-HIV-1 Fab 447-52D in complex with V3 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Q1J
- Type
- protein
- Length
- 912 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab 447-52D, light chain; Fab 447-52D, heavy chain; GP120 V3 peptide
- Pockets
- 11 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, M | Fab 447-52D, light chain | protein | 215 | 8% helix, 49% strand | — |
| H, I | Fab 447-52D, heavy chain | protein | 231 | 9% helix, 54% strand | — |
| P, Q | GP120 V3 peptide | protein | 10 | 0% helix, 30% strand | — |
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 198 | 0.69 | 0.86 | 45 | empty |
| 2 | 560 | 0.63 | 0.75 | 74 | empty |
| 3 | 392 | 0.58 | 0.75 | 54 | empty |
| 4 | 222 | 0.52 | 0.77 | 27 | empty |
| 5 | 208 | 0.50 | 0.76 | 27 | empty |
Interfaces
10 interfaces between chains.
- L–H · 1814 Ų buried · 16 hydrogen bonds · protein-protein
- M–I · 1784 Ų buried · 11 hydrogen bonds · protein-protein
- I–Q · 546 Ų buried · 9 hydrogen bonds · protein-protein
- H–P · 530 Ų buried · 8 hydrogen bonds · protein-protein
- H–I · 488 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1Q1J · Crystal Structure Analysis of anti-HIV-1 Fab 447-52D in complex with V3 peptide · the same entry in another collection · chain L against L, 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 1Q1J · PDBe 1Q1J
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