Research workbench
Crystal structure of anti-HIV-1 V3 Fab 311-11D in complex with a HIV-1 GP120 V3 peptide from mn strain
Analyse Crystal structure of anti-HIV-1 V3 Fab 311-11D 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
- 6DB6
- Type
- protein
- Length
- 453 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human monoclonal anti-HIV-1 GP120 V3 antibody 311-11D Fab heavy chain; Human monoclonal…
- Ligands
- NAG, BMA, MAN, FCA
- Pockets
- 4 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Human monoclonal anti-HIV-1 GP120 V3 antibody 311-11D Fab heavy chain | protein | 226 | 9% helix, 50% strand | — |
| L | Human monoclonal anti-HIV-1 GP120 V3 antibody 311-11D Fab light chain | protein | 213 | 6% helix, 49% strand | — |
| P | HIV-1 GP120 V3 peptide from mn strain | protein | 14 | 0% helix, 64% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains H
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
- FCA · alpha-D-fucopyranose · sugar · chains H, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 393 | 0.55 | 0.74 | 54 | empty |
| 2 | 129 | 0.47 | 0.78 | 23 | empty |
| 3 | 106 | 0.41 | 0.77 | 25 | empty |
| 4 | 81 | 0.33 | 0.74 | 21 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1995 Ų buried · 23 hydrogen bonds · protein-protein
- H–P · 464 Ų buried · 2 hydrogen bonds · protein-protein
- L–P · 399 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6DB6 · Crystal structure of anti-HIV-1 V3 Fab 311-11D in complex with a HIV-1 gp120 V3 peptide… · 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 6DB6 · PDBe 6DB6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.