Research workbench
Crystal structure of anti-HIV-1 V3 Fab TA6 in complex with a HIV-1 GP120 V3 peptide from NY5 strain
Analyse Crystal structure of anti-HIV-1 V3 Fab TA6 in complex with a HIV-1 GP120 V3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DB5
- Type
- protein
- Length
- 906 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human monoclonal anti-HIV-1 GP120 V3 antibody TA6 Fab heavy chain; Human monoclonal…
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, I | Human monoclonal anti-HIV-1 GP120 V3 antibody TA6 Fab heavy chain | protein | 228 | 5% helix, 51% strand | — |
| L, M | Human monoclonal anti-HIV-1 GP120 V3 antibody TA6 Fab light chain | protein | 211 | 8% helix, 50% strand | — |
| P, Q | HIV-1 GP120 V3 peptide from NY5 strain | protein | 14 | 0% helix, 57% strand | — |
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 847 | 0.70 | 0.76 | 99 | empty |
| 2 | 464 | 0.57 | 0.73 | 56 | empty |
| 3 | 166 | 0.46 | 0.76 | 17 | empty |
| 4 | 71 | 0.45 | 0.83 | 22 | empty |
| 5 | 136 | 0.44 | 0.76 | 28 | empty |
Interfaces
8 interfaces between chains.
- I–M · 1944 Ų buried · 18 hydrogen bonds · protein-protein
- H–L · 1940 Ų buried · 21 hydrogen bonds · protein-protein
- I–Q · 455 Ų buried · 3 hydrogen bonds · protein-protein
- H–P · 448 Ų buried · 2 hydrogen bonds · protein-protein
- L–P · 414 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6DB5 · Crystal structure of anti-HIV-1 V3 Fab TA6 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
- Elsewhere: RCSB PDB 6DB5 · PDBe 6DB5
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