Research workbench
HIV-1 in core domain in complex with (1-methyl-5-phenyl-1H-pyrazol-4- YL)METHANOL
Analyse HIV-1 in core domain in complex with (1-methyl-5-phenyl-1H-pyrazol-4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VQ6
- Type
- protein
- Length
- 288 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pol polyprotein
- UniProt
- Q72498
- Ligands
- BCK, CD, SO4
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pol polyprotein | protein | 145 | 47% helix, 23% strand | Q72498 |
| B | Pol polyprotein | protein | 143 | 49% helix, 22% strand | Q72498 |
Ligands and binding sites
- BCK · (1-methyl-5-phenyl-1H-pyrazol-4-yl)methanol · ligand · chains A
- CD · Cadmium ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.71 | 0.98 | 13 | empty |
| 2 | 135 | 0.48 | 0.78 | 19 | empty |
| 3 | 112 | 0.48 | 0.80 | 20 | empty |
| 4 | 60 | 0.46 | 0.84 | 17 | empty |
| 5 | 103 | 0.43 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1538 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 3VQ6 · HIV-1 IN core domain in complex with (1-methyl-5-phenyl-1H-pyrazol-4-yl)methanol · 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 Q72498
- Elsewhere: RCSB PDB 3VQ6 · PDBe 3VQ6 · UniProt Q72498
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