Research workbench
HIV protease, pseudo-symmetric inhibitors
Analyse HIV protease, pseudo-symmetric inhibitors in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GGX
- Type
- protein
- Length
- 792 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- V-1 protease
- UniProt
- Q9Q2G8
- Ligands
- GGX
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | V-1 protease | protein | 99 | 7% helix, 54% strand | Q9Q2G8 |
Ligands and binding sites
- GGX · methyl [(1S)-1-{[(1R,3S,4S)-4-{[(2S)-3,3-dimethyl-2-{3-[(6-methylpyridin-2-yl)methyl]-2-oxo-2,3-dihydro-1H-imidazol-1-yl}butanoyl]amino}-3-hydroxy-5-phenyl-1-(4-pyridin-2-ylbenzyl)pentyl]carbamoyl}-2,2-dimethylpropyl]carbamate · ligand · 4 copies · chains G, H, A, B, C, E, F, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 517 | 0.73 | 0.81 | 44 | GGX |
| 2 | 517 | 0.71 | 0.80 | 50 | GGX |
| 3 | 430 | 0.69 | 0.81 | 35 | GGX |
| 4 | 401 | 0.69 | 0.81 | 33 | GGX |
| 5 | 228 | 0.53 | 0.77 | 26 | empty |
Interfaces
11 interfaces between chains.
- A–B · 1837 Ų buried · 32 hydrogen bonds · protein-protein
- E–F · 1828 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 1828 Ų buried · 45 hydrogen bonds · protein-protein
- G–H · 1811 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 513 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3GGX · HIV Protease, pseudo-symmetric inhibitors · 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 Q9Q2G8
- Elsewhere: RCSB PDB 3GGX · PDBe 3GGX · UniProt Q9Q2G8
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