MolNFT v1 · #64877 · protein
HIV protease inhibitors with pseudo-symmetric cores
3GGA · V-1 protease: “HIV protease inhibitors with pseudo-symmetric cores”. X-ray diffraction, 1 ligand (GGW), 4 pockets (best druggability 0.71). MolNFT v1 #64877 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3GGA
- Type
- protein
- Length
- 594 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- V-1 protease
- UniProt
- Q9Q2G8
- Ligands
- GGW
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, H, A, B, C, D | V-1 protease | protein | 99 | 4% helix, 54% strand | Q9Q2G8 |
Ligands and binding sites
- GGW · methyl [(1S,4S,5S,7S,10S)-4-benzyl-1,10-di-tert-butyl-5-hydroxy-2,9,12-trioxo-7-(4-pyridin-2-ylbenzyl)-13-oxa-3,8,11-triazatetradec-1-yl]carbamate · ligand · chains G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 397 | 0.71 | 0.82 | 33 | empty |
| 2 | 411 | 0.71 | 0.82 | 38 | GGW |
| 3 | 426 | 0.70 | 0.81 | 45 | empty |
| 4 | 173 | 0.47 | 0.76 | 32 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1837 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 1828 Ų buried · 41 hydrogen bonds · protein-protein
- G–H · 1823 Ų buried · 37 hydrogen bonds · protein-protein
- G–A · 245 Ų buried · 7 hydrogen bonds · protein-protein
- H–A · 129 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3GGA · HIV Protease inhibitors with pseudo-symmetric cores · the same entry in another collection · chain G against G, 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 3GGA · PDBe 3GGA · UniProt Q9Q2G8
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