MolNFT v1 · #143394 · protein
Structure of the native full-length HIV-1 capsid protein in complex with CPSF6 peptide
6AY9: “Structure of the native full-length HIV-1 capsid protein in complex with CPSF6 peptide”. X-ray diffraction, 2 ligands (IOD, CL), 1 pocket (best druggability 0.38). MolNFT v1 #143394 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6AY9
- Type
- protein
- Length
- 230 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 capsid protein; Cleavage and polyadenylation specificity factor subunit 6
- UniProt
- B6DRA0, Q16630
- Ligands
- IOD, CL
- Pockets
- 1 · best druggability 0.38
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV-1 capsid protein | protein | 218 | 60% helix, 2% strand | B6DRA0 |
| B | Cleavage and polyadenylation specificity factor subunit 6 | protein | 12 | 0% helix, 0% strand | Q16630 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 61 | 0.38 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 537 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6AY9 · Structure of the native full-length HIV-1 capsid protein in complex with CPSF6 peptide · the same entry in another collection · chain A against A, TM-score 1.00
- Q16630 · AlphaFold monomer V2.0 prediction for cleavage and polyadenylation specificity factor… · a predicted model of the same protein · chain B against A, TM-score 0.37
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
- Every structure of UniProt Q16630
- Elsewhere: RCSB PDB 6AY9 · PDBe 6AY9 · UniProt B6DRA0 · UniProt Q16630
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