Research workbench
HIV-1 in core domain in complex with 6-fluoro-4H-1,3-benzodioxine-8- carboxylic acid
Analyse HIV-1 in core domain in complex with 6-fluoro-4H-1,3-benzodioxine-8- carboxylic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VQB
- Type
- protein
- Length
- 282 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pol polyprotein
- UniProt
- Q72498
- Ligands
- FBG, CD, SO4
- Pockets
- 5 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pol polyprotein | protein | 142 | 46% helix, 25% strand | Q72498 |
| B | Pol polyprotein | protein | 140 | 48% helix, 24% strand | Q72498 |
Ligands and binding sites
- FBG · 6-fluoro-4H-1,3-benzodioxine-8-carboxylic acid · ligand · 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
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 157 | 0.52 | 0.79 | 18 | empty |
| 2 | 108 | 0.46 | 0.79 | 21 | FBG |
| 3 | 71 | 0.46 | 0.82 | 19 | empty |
| 4 | 106 | 0.44 | 0.78 | 16 | empty |
| 5 | 126 | 0.44 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1571 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 3VQB · HIV-1 IN core domain in complex with 6-fluoro-4H-1,3-benzodioxine-8-carboxylic acid · 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 3VQB · PDBe 3VQB · UniProt Q72498
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