MolNFT v1 · #106313 · protein
Crystal structure of multidrug-resistant clinical isolate A02 HIV-1 protease in complex with non-peptidic inhibitor, GRL0519
4RVI: “Crystal structure of multidrug-resistant clinical isolate A02 HIV-1 protease in complex with non-peptidic…”. X-ray diffraction, 1 ligand (G52), 3 pockets (best druggability 0.71). MolNFT v1 #106313 on GenesisL1: 3D structure…
- PDB
- 4RVI
- Type
- protein
- Length
- 396 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 protease
- UniProt
- Q9J006
- Ligands
- G52
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | HIV-1 protease | protein | 99 | 7% helix, 55% strand | Q9J006 |
Ligands and binding sites
- G52 · (3r,3as,3br,6as,7as)-octahydrodifuro[2,3-B:3',2'-d]furan-3-yl [(1S,2R)-1-benzyl-2-hydroxy-3-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl) amino}propyl]carbamate · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 420 | 0.71 | 0.82 | 42 | G52 |
| 2 | 403 | 0.71 | 0.82 | 41 | G52 |
| 3 | 56 | 0.29 | 0.75 | 11 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1878 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 1860 Ų buried · 37 hydrogen bonds · protein-protein
- A–D · 131 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4RVI · Crystal structure of multidrug-resistant clinical isolate A02 HIV-1 protease in complex… · 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 Q9J006
- Elsewhere: RCSB PDB 4RVI · PDBe 4RVI · UniProt Q9J006
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