MolNFT v1 · #164016 · protein
Structure of the native full-length HIV-1 capsid protein A92E in helical assembly (-13,12)
6SKM · Gag protein: “Structure of the native full-length HIV-1 capsid protein A92E in helical assembly (-13,12)”. Electron microscopy, 20 pockets (best druggability 0.76). MolNFT v1 #164016 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6SKM
- Type
- protein
- Length
- 1,320 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gag protein
- UniProt
- Q71B32
- Pockets
- 20 · best druggability 0.76
Structure
electron microscopy · 1 distinct chain · 59% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Gag protein | protein | 220 | 59% helix, 3% strand | Q71B32 |
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 658 | 0.76 | 0.82 | 92 | empty |
| 2 | 816 | 0.76 | 0.80 | 90 | empty |
| 3 | 922 | 0.76 | 0.79 | 103 | empty |
| 4 | 711 | 0.75 | 0.80 | 82 | empty |
| 5 | 1077 | 0.72 | 0.76 | 88 | empty |
Interfaces
9 interfaces between chains.
- A–F · 1285 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1270 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 1171 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1157 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 1142 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6SKM · Structure of the native full-length HIV-1 capsid protein A92E in helical assembly (-13,12) · 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 Q71B32
- Elsewhere: RCSB PDB 6SKM · PDBe 6SKM · UniProt Q71B32
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