MolNFT v1 · #80158 · protein
HIV-1 protease - epoxydic inhibitor complex (pH 9 - orthorombic crystal form P212121)
3TOH · Gag-pol polyprotein: “HIV-1 protease - epoxydic inhibitor complex (pH 9 - orthorombic crystal form P212121)”. X-ray diffraction, 1 ligand (079), 1 pocket (best druggability 0.71). MolNFT v1 #80158 on GenesisL1: 3D structure, binding…
- PDB
- 3TOH
- Type
- protein
- Length
- 198 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gag-pol polyprotein
- EC
- 3.4.23.16, 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2
- UniProt
- P03367
- Ligands
- 079
- Pockets
- 1 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Gag-pol polyprotein (EC 3.4.23.16, 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2) | protein | 99 | 4% helix, 56% strand | P03367 |
Ligands and binding sites
- 079 · (S)-N-((2S,3S,4R,5R)-4-amino-3,5-dihydroxy-1,6-diphenylhexan-2-yl)-3-methyl-2-(2-phenoxyacetamido)butanamide · ligand · chains A, B
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 355 | 0.71 | 0.83 | 35 | 079 |
Interfaces
1 interface between chains.
- A–B · 1859 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- 3TOH · HIV-1 Protease - Epoxydic Inhibitor Complex (pH 9 - Orthorombic Crystal form P212121) · 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 P03367
- Elsewhere: RCSB PDB 3TOH · PDBe 3TOH · UniProt P03367
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