Research workbench
Structure of the native full-length HIV-1 capsid protein in complex with NUP153 peptide
Analyse Structure of the native full-length HIV-1 capsid protein in complex with NUP153… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AYA
- Type
- protein
- Length
- 223 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 capsid protein; Nuclear pore complex protein NUP153
- UniProt
- P12493, P49790
- Ligands
- IOD, CL
- Pockets
- 1 · best druggability 0.28
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV-1 capsid protein | protein | 214 | 62% helix, 2% strand | P12493 |
| B | Nuclear pore complex protein NUP153 | protein | 9 | 0% helix, 0% strand | P49790 |
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 | 51 | 0.28 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 306 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6AYA · Structure of the native full-length HIV-1 capsid protein in complex with Nup153 peptide · the same entry in another collection · chain A against A, TM-score 1.00
- P49790 · AlphaFold monomer V2.0 prediction for nuclear pore complex protein NUP153 (P49790) · 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 P12493
- Every structure of UniProt P49790
- Elsewhere: RCSB PDB 6AYA · PDBe 6AYA · UniProt P12493 · UniProt P49790
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