Research workbench
HIV-1 ca hexamer with NUP153 peptide - R3 crystal form
Analyse HIV-1 ca hexamer with NUP153 peptide - R3 crystal form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TSV
- Type
- protein
- Length
- 438 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 ca protein; Nuclear pore complex protein NUP153
- UniProt
- P12493, P49790
- Ligands
- FLU
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 60% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV-1 ca protein | protein | 209 | 64% helix, 3% strand | P12493 |
| B | HIV-1 ca protein | protein | 219 | 60% helix, 3% strand | P12493 |
| D | Nuclear pore complex protein NUP153 | protein | 10 | 0% helix, 0% strand | P49790 |
Ligands and binding sites
- FLU · 2-(6-hydroxy-3-oxo-3H-xanthen-9-yl)-benzoic acid · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 640 | 0.68 | 0.77 | 67 | empty |
| 2 | 130 | 0.56 | 0.82 | 26 | empty |
| 3 | 181 | 0.51 | 0.78 | 27 | empty |
| 4 | 67 | 0.35 | 0.77 | 17 | empty |
| 5 | 52 | 0.28 | 0.75 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1220 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 385 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 339 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5TSV · HIV-1 CA hexamer with NUP153 peptide - R3 crystal form · 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 D against A, TM-score 0.36
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 5TSV · PDBe 5TSV · UniProt P12493 · UniProt P49790
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