MolNFT v1 · #82538 · protein
HIV-1 in core domain in complex with 6-fluoro-1,3-benzothiazol-2-amine
3VQ9 · Pol polyprotein: “HIV-1 in core domain in complex with 6-fluoro-1,3-benzothiazol-2-amine”. X-ray diffraction, 1 ligand (FBB), 7 pockets (best druggability 0.71). MolNFT v1 #82538 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3VQ9
- Type
- protein
- Length
- 442 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pol polyprotein
- UniProt
- Q72498
- Ligands
- FBB
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pol polyprotein | protein | 142 | 47% helix, 20% strand | Q72498 |
| B | Pol polyprotein | protein | 142 | 52% helix, 20% strand | Q72498 |
| C | Pol polyprotein | protein | 158 | 47% helix, 23% strand | Q72498 |
Ligands and binding sites
- FBB · 6-fluoro-1,3-benzothiazol-2-amine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.71 | 0.97 | 21 | empty |
| 2 | 163 | 0.50 | 0.77 | 20 | empty |
| 3 | 111 | 0.48 | 0.80 | 18 | empty |
| 4 | 164 | 0.47 | 0.77 | 32 | empty |
| 5 | 99 | 0.44 | 0.78 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1549 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 354 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 45 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3VQ9 · HIV-1 IN core domain in complex with 6-fluoro-1,3-benzothiazol-2-amine · 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 3VQ9 · PDBe 3VQ9 · UniProt Q72498
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.