MolNFT v1 · #164017 · protein
Structure of the native full-length HIV-1 capsid protein in helical assembly (-13,8)
6SKN · Gag protein: “Structure of the native full-length HIV-1 capsid protein in helical assembly (-13,8)”. Electron microscopy, 20 pockets (best druggability 0.75). MolNFT v1 #164017 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6SKN
- Type
- protein
- Length
- 3,960 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gag protein
- UniProt
- Q71B32
- Pockets
- 20 · best druggability 0.75
Structure
electron microscopy · 1 distinct chain · 59% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, I, K, M, O, Q, H, J, L, N, P, R | Gag protein | protein | 220 | 59% helix, 3% strand | Q71B32 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 870 | 0.75 | 0.79 | 107 | empty |
| 2 | 771 | 0.74 | 0.79 | 84 | empty |
| 3 | 943 | 0.72 | 0.76 | 87 | empty |
| 4 | 537 | 0.69 | 0.79 | 60 | empty |
| 5 | 509 | 0.69 | 0.79 | 59 | empty |
Interfaces
25 interfaces between chains.
- K–M · 1126 Ų buried · 6 hydrogen bonds · protein-protein
- G–Q · 1118 Ų buried · 10 hydrogen bonds · protein-protein
- L–N · 1105 Ų buried · 5 hydrogen bonds · protein-protein
- A–F · 1104 Ų buried · 11 hydrogen bonds · protein-protein
- H–R · 1099 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 6SKN · Structure of the native full-length HIV-1 capsid protein in helical assembly (-13,8) · 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 6SKN · PDBe 6SKN · UniProt Q71B32
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