MolNFT v1 · #82534 · protein
HIV-1 in core domain in complex with N-methyl-1-(4-methyl-2-phenyl-1, 3-thiazol-5-YL)METHANAMINE
3VQ5 · Pol polyprotein: “HIV-1 in core domain in complex with N-methyl-1-(4-methyl-2-phenyl-1, 3-thiazol-5-YL)METHANAMINE”. X-ray diffraction, 4 ligands (MMJ, CD, SO4), 5 pockets (best druggability 0.49). MolNFT v1 #82534 on GenesisL1: 3D…
- PDB
- 3VQ5
- Type
- protein
- Length
- 265 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pol polyprotein
- UniProt
- Q72498
- Ligands
- MMJ, CD, SO4, CL
- Pockets
- 5 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pol polyprotein | protein | 133 | 50% helix, 21% strand | Q72498 |
| B | Pol polyprotein | protein | 132 | 51% helix, 21% strand | Q72498 |
Ligands and binding sites
- MMJ · N-methyl-1-(4-methyl-2-phenyl-1,3-thiazol-5-yl)methanamine · ligand · 2 copies · chains A, B
- CD · Cadmium ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 95 | 0.49 | 0.82 | 22 | MMJ |
| 2 | 156 | 0.49 | 0.77 | 19 | empty |
| 3 | 89 | 0.43 | 0.79 | 22 | MMJ |
| 4 | 88 | 0.41 | 0.78 | 15 | empty |
| 5 | 85 | 0.37 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1409 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 3VQ5 · HIV-1 IN core domain in complex with N-METHYL-1-(4-METHYL-2-PHENYL-1,3-THIAZOL-5-YL)METHAN… · 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 3VQ5 · PDBe 3VQ5 · UniProt Q72498
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