Research workbench
A novel HIV-1 nef dimer interface induced by a single octyl-glucoside molecule
Analyse A novel HIV-1 nef dimer interface induced by a single octyl-glucoside molecule in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6B72
- Type
- protein
- Length
- 729 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein nef
- UniProt
- P03407
- Pockets
- 11 · best druggability 0.60
Structure
x-ray diffraction · 5 distinct chains · 41% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein nef | protein | 124 | 41% helix, 11% strand | P03407 |
| B | Protein nef | protein | 121 | 40% helix, 13% strand | P03407 |
| C, D | Protein nef | protein | 122 | 42% helix, 14% strand | P03407 |
| E | Protein nef | protein | 119 | 44% helix, 13% strand | P03407 |
| F | Protein nef | protein | 121 | 40% helix, 13% strand | P03407 |
Ligands and binding sites
- BOG · octyl beta-D-glucopyranoside · additive · 3 copies · chains A, B, C, E, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 166 | 0.60 | 0.83 | 24 | BOG |
| 2 | 166 | 0.59 | 0.82 | 22 | BOG |
| 3 | 165 | 0.59 | 0.82 | 23 | BOG |
| 4 | 85 | 0.56 | 0.86 | 18 | empty |
| 5 | 215 | 0.54 | 0.78 | 31 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1140 Ų buried · 15 hydrogen bonds · protein-protein
- D–F · 1114 Ų buried · 14 hydrogen bonds · protein-protein
- C–E · 1095 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 353 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 73 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6B72 · A novel HIV-1 Nef dimer interface induced by a single octyl-glucoside molecule · the same entry in another collection · chain A against A, 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 P03407
- Elsewhere: RCSB PDB 6B72 · PDBe 6B72 · UniProt P03407
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