Research workbench
X-ray structure of pentameric HIV-1 ca
Analyse X-ray structure of pentameric HIV-1 ca in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3P05
- Type
- protein
- Length
- 1,033 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 ca
- UniProt
- Q72497
- Ligands
- IOD
- Pockets
- 16 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 64% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV-1 ca | protein | 210 | 62% helix, 0% strand | Q72497 |
| B, C | HIV-1 ca | protein | 209 | 61% helix, 1% strand | Q72497 |
| D | HIV-1 ca | protein | 206 | 65% helix, 3% strand | Q72497 |
| E | HIV-1 ca | protein | 199 | 67% helix, 0% strand | Q72497 |
Ligands and binding sites
- IOD · Iodide ion · ion · 10 copies · chains A, E, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 851 | 0.76 | 0.80 | 78 | empty |
| 2 | 466 | 0.63 | 0.76 | 60 | empty |
| 3 | 365 | 0.59 | 0.76 | 60 | empty |
| 4 | 298 | 0.59 | 0.78 | 32 | IOD |
| 5 | 272 | 0.58 | 0.78 | 33 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1212 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 1110 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1089 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 1067 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 1066 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 3P05 · X-ray structure of pentameric HIV-1 CA · 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 Q72497
- Elsewhere: RCSB PDB 3P05 · PDBe 3P05 · UniProt Q72497
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