MolNFT v1 · #82539 · protein
HIV-1 in core domain in complex with 1-benzothiophen-6-amine 1,1- dioxide
3VQA · Pol polyprotein: “HIV-1 in core domain in complex with 1-benzothiophen-6-amine 1,1- dioxide”. X-ray diffraction, 5 ligands (MWP, GLC, FRU), 4 pockets (best druggability 0.60). MolNFT v1 #82539 on GenesisL1: 3D structure, binding…
- PDB
- 3VQA
- Type
- protein
- Length
- 280 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pol polyprotein
- UniProt
- Q72498
- Ligands
- MWP, GLC, FRU, CD, SO4
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pol polyprotein | protein | 141 | 46% helix, 26% strand | Q72498 |
| B | Pol polyprotein | protein | 139 | 50% helix, 22% strand | Q72498 |
Ligands and binding sites
- MWP · 1-benzothiophen-6-amine 1,1-dioxide · ligand · chains A, B
- GLC · alpha-D-glucopyranose · sugar · chains A, B
- FRU · beta-D-fructofuranose · sugar · chains A, B
- 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
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 294 | 0.60 | 0.78 | 32 | GLC, FRU |
| 2 | 111 | 0.48 | 0.79 | 22 | empty |
| 3 | 83 | 0.44 | 0.80 | 16 | empty |
| 4 | 64 | 0.43 | 0.81 | 18 | MWP |
Interfaces
1 interface between chains.
- A–B · 1518 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 3VQA · HIV-1 IN core domain in complex with 1-benzothiophen-6-amine 1,1-dioxide · 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 3VQA · PDBe 3VQA · UniProt Q72498
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