Research workbench
Crystal structure of the 3D6 antibody fragment bound to the HIV-1 GP41 immunodominant region
Analyse Crystal structure of the 3D6 antibody fragment bound to the HIV-1 GP41… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7N08
- Type
- protein
- Length
- 1,368 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 GP41 immunodominant region; Fab 3D6 heavy chain; Fab 3D6 light chain
- Pockets
- 14 · best druggability 0.60
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, F, E | HIV-1 GP41 immunodominant region | protein | 11 | 0% helix, 9% strand | — |
| H | Fab 3D6 heavy chain | protein | 233 | 8% helix, 54% strand | — |
| L, B, D | Fab 3D6 light chain | protein | 212 | 7% helix, 50% strand | — |
| A | Fab 3D6 heavy chain | protein | 234 | 8% helix, 54% strand | — |
| C | Fab 3D6 heavy chain | protein | 232 | 8% helix, 54% strand | — |
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 487 | 0.60 | 0.75 | 49 | empty |
| 2 | 475 | 0.58 | 0.73 | 63 | empty |
| 3 | 375 | 0.57 | 0.75 | 49 | empty |
| 4 | 338 | 0.55 | 0.75 | 40 | empty |
| 5 | 71 | 0.50 | 0.85 | 24 | empty |
Interfaces
12 interfaces between chains.
- H–L · 2093 Ų buried · 16 hydrogen bonds · protein-protein
- D–C · 2089 Ų buried · 17 hydrogen bonds · protein-protein
- B–A · 2053 Ų buried · 19 hydrogen bonds · protein-protein
- E–A · 586 Ų buried · 7 hydrogen bonds · protein-protein
- G–C · 586 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide (disulfide).
Compared structures
- 7N08 · Crystal structure of the 3D6 antibody fragment bound to the HIV-1 gp41 immunodominant… · the same entry in another collection · chain G against G, 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 7N08 · PDBe 7N08
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