MolNFT v1 · #82552 · protein
HIV-1 in core domain in complex with 2,3-dihydro-1,4-benzodioxin-5- ylmethanol
3VQP · Pol polyprotein: “HIV-1 in core domain in complex with 2,3-dihydro-1,4-benzodioxin-5- ylmethanol”. X-ray diffraction, 4 ligands (DBJ, CD, SO4), 6 pockets (best druggability 0.70). MolNFT v1 #82552 on GenesisL1: 3D structure, binding…
- PDB
- 3VQP
- Type
- protein
- Length
- 281 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pol polyprotein
- UniProt
- Q72498
- Ligands
- DBJ, CD, SO4, CL
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pol polyprotein | protein | 141 | 46% helix, 25% strand | Q72498 |
| B | Pol polyprotein | protein | 140 | 48% helix, 24% strand | Q72498 |
Ligands and binding sites
- DBJ · 2,3-dihydro-1,4-benzodioxin-5-ylmethanol · ligand · chains A, B
- CD · Cadmium ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A
- CL · Chloride 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 | 53 | 0.70 | 0.98 | 14 | empty |
| 2 | 148 | 0.50 | 0.78 | 18 | empty |
| 3 | 95 | 0.48 | 0.81 | 21 | empty |
| 4 | 99 | 0.47 | 0.80 | 20 | DBJ |
| 5 | 116 | 0.42 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1438 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3VQP · HIV-1 IN core domain in complex with 2,3-dihydro-1,4-benzodioxin-5-ylmethanol · 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 3VQP · PDBe 3VQP · UniProt Q72498
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