MolNFT v1 · #106314 · protein
Crystal structure of multidrug-resistant clinical isolate A02 HIV-1 protease in complex with amprenavir
4RVJ: “Crystal structure of multidrug-resistant clinical isolate A02 HIV-1 protease in complex with amprenavir”. X-ray diffraction, 1 ligand (478), 2 pockets (best druggability 0.73). MolNFT v1 #106314 on GenesisL1: 3D structure, binding…
- PDB
- 4RVJ
- 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
- 478
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | HIV-1 protease | protein | 99 | 7% helix, 58% strand | Q9J006 |
Ligands and binding sites
- 478 · {3-[(4-amino-benzenesulfonyl)-isobutyl-amino]-1-benzyl-2-hydroxy-propyl}-carbamic acid tetrahydro-furan-3-yl ester · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 373 | 0.73 | 0.84 | 40 | 478 |
| 2 | 379 | 0.72 | 0.83 | 41 | 478 |
Interfaces
5 interfaces between chains.
- A–B · 1876 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 1862 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 20 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 19 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 15 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4RVJ · 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 4RVJ · PDBe 4RVJ · UniProt Q9J006
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