MolNFT v1 · #146223 · protein
Crystal structure of anti-HIV-1 V3 Fab 1334 in complex with a HIV-1 GP120 V3 peptide from mn strain
6DB7 · Human monoclonal anti-HIV-1 GP120 V3 antibody 1334 Fab…: “Crystal structure of anti-HIV-1 V3 Fab 1334 in complex with a HIV-1 GP120 V3 peptide from mn strain”. X-ray diffraction, 11 pockets (best druggability 0.75). MolNFT v1…
- PDB
- 6DB7
- Type
- protein
- Length
- 914 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human monoclonal anti-HIV-1 GP120 V3 antibody 1334 Fab heavy chain; Human monoclonal…
- UniProt
- A9Q0A0
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 6% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Human monoclonal anti-HIV-1 GP120 V3 antibody 1334 Fab heavy chain | protein | 234 | 8% helix, 47% strand | — |
| L | Human monoclonal anti-HIV-1 GP120 V3 antibody 1334 Fab light chain | protein | 211 | 7% helix, 48% strand | — |
| P, Q | HIV-1 GP120 V3 peptide from mn strain | protein | 13 | 0% helix, 54% strand | A9Q0A0 |
| I | Human monoclonal anti-HIV-1 GP120 V3 antibody 1334 Fab heavy chain | protein | 233 | 5% helix, 47% strand | — |
| M | Human monoclonal anti-HIV-1 GP120 V3 antibody 1334 Fab light chain | protein | 210 | 6% helix, 50% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 12 copies · chains H, L, I, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 472 | 0.75 | 0.84 | 50 | GOL |
| 2 | 602 | 0.70 | 0.79 | 54 | GOL |
| 3 | 228 | 0.65 | 0.83 | 38 | empty |
| 4 | 175 | 0.52 | 0.78 | 23 | empty |
| 5 | 107 | 0.51 | 0.82 | 19 | empty |
Interfaces
10 interfaces between chains.
- I–M · 1952 Ų buried · 28 hydrogen bonds · protein-protein
- H–L · 1837 Ų buried · 19 hydrogen bonds · protein-protein
- H–P · 564 Ų buried · 7 hydrogen bonds · protein-protein
- I–Q · 545 Ų buried · 8 hydrogen bonds · protein-protein
- L–P · 383 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6DB7 · Crystal structure of anti-HIV-1 V3 Fab 1334 in complex with a HIV-1 gp120 V3 peptide from… · 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
- Every structure of UniProt A9Q0A0
- Elsewhere: RCSB PDB 6DB7 · PDBe 6DB7 · UniProt A9Q0A0
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