MolNFT v1 · #191107 · protein
Crystal structure of HIV-1 capsid IP6-CPSF6 complex
7ZUD · Capsid protein P24: “Crystal structure of HIV-1 capsid IP6-CPSF6 complex”. X-ray diffraction, 1 ligand (IHP), 1 pocket (best druggability 0.32). MolNFT v1 #191107 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7ZUD
- Type
- protein
- Length
- 223 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein P24; Cleavage and polyadenylation specificity factor subunit 6
- UniProt
- P12497, Q16630
- Ligands
- IHP
- Pockets
- 1 · best druggability 0.32
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein P24 | protein | 210 | 58% helix, 3% strand | P12497 |
| M | Cleavage and polyadenylation specificity factor subunit 6 | protein | 13 | 0% helix, 0% strand | Q16630 |
Ligands and binding sites
- IHP · Inositol hexakisphosphate · ligand · 2 copies · chains A
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 | 58 | 0.32 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–M · 501 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 7ZUD · Crystal structure of HIV-1 capsid IP6-CPSF6 complex · 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 M against A, TM-score 0.27
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 P12497
- Every structure of UniProt Q16630
- Elsewhere: RCSB PDB 7ZUD · PDBe 7ZUD · UniProt P12497 · UniProt Q16630
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