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Crystal structure of the HIV capsid hexamer bound to the small molecule long-acting inhibitor, gs-6207
Analyse Crystal structure of the HIV capsid hexamer bound to the small molecule… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6V2F
- Type
- protein
- Length
- 1,213 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 capsid
- UniProt
- B6DRA0
- Ligands
- QNG
- Pockets
- 12 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 63% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | HIV-1 capsid | protein | 206 | 63% helix, 1% strand | B6DRA0 |
| B | HIV-1 capsid | protein | 195 | 63% helix, 1% strand | B6DRA0 |
| C | HIV-1 capsid | protein | 196 | 61% helix, 2% strand | B6DRA0 |
| D | HIV-1 capsid | protein | 207 | 64% helix, 1% strand | B6DRA0 |
| F | HIV-1 capsid | protein | 203 | 64% helix, 1% strand | B6DRA0 |
Ligands and binding sites
- QNG · N-[(1S)-1-(3-{4-chloro-3-[(methylsulfonyl)amino]-1-(2, 2,2-trifluoroethyl)-1H-indazol-7-yl}-6-[3-methyl-3-(methylsulfonyl)but-1-yn-1-yl]pyridin-2-yl)-2-(3,5-difluorophenyl)ethyl]-2-[(3bs,4ar)-5,5-difluoro-3-(trifluoromethyl)-3B,4,4A,5-tetrahydro-1H-cyclopropa[3,4]cyclopenta[1,2-c]pyrazol-1-yl]acetamide · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 678 | 0.71 | 0.78 | 67 | QNG |
| 2 | 84 | 0.40 | 0.78 | 16 | empty |
| 3 | 73 | 0.38 | 0.78 | 18 | empty |
| 4 | 77 | 0.38 | 0.77 | 19 | empty |
| 5 | 87 | 0.37 | 0.76 | 17 | empty |
Interfaces
2 interfaces between chains.
- E–F · 1092 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 409 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 6V2F · Crystal structure of the HIV capsid hexamer bound to the small molecule long-acting… · 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 B6DRA0
- Elsewhere: RCSB PDB 6V2F · PDBe 6V2F · UniProt B6DRA0
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