Research workbench
HIV-1 protease - epoxydic inhibitor complex (pH 9 - monoclinic crystal form P21)
Analyse HIV-1 protease - epoxydic inhibitor complex (pH 9 - monoclinic crystal form P21) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TOG
- Type
- protein
- Length
- 396 residues
- Chains
- 4
- 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
- 4 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 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, 55% 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 · 2 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 649 | 0.74 | 0.80 | 57 | 079 |
| 2 | 348 | 0.70 | 0.83 | 35 | 079 |
| 3 | 163 | 0.46 | 0.75 | 16 | empty |
| 4 | 64 | 0.33 | 0.76 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1870 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 1844 Ų buried · 37 hydrogen bonds · protein-protein
- B–D · 320 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 147 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 71 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3TOG · HIV-1 Protease - Epoxydic Inhibitor Complex (pH 9 - Monoclinic Crystal form P21) · the same entry in another collection · chain B against B, 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 3TOG · PDBe 3TOG · UniProt P03367
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