MolNFT v1 · #82197 · protein
Crystal structure of HIV-1 protease mutant V82A with novel P1'-ligands grl-02031
3VFA: “Crystal structure of HIV-1 protease mutant V82A with novel P1'-ligands grl-02031”. X-ray diffraction, 3 ligands (031, NA, CL), 1 pocket (best druggability 0.72). MolNFT v1 #82197 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3VFA
- Type
- protein
- Length
- 198 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease
- EC
- 3.4.23.16
- UniProt
- P0C6F2
- Ligands
- 031, NA, CL
- Pockets
- 1 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protease (EC 3.4.23.16) | protein | 99 | 7% helix, 55% strand | P0C6F2 |
Ligands and binding sites
- 031 · (3aS,5R,6aR)-hexahydro-2H-cyclopenta[b]furan-5-yl [(1S,2R)-1-benzyl-2-hydroxy-3-([(4-methoxyphenyl)sulfonyl]{[(2R)-5-oxopyrrolidin-2-yl]methyl}amino)propyl]carbamate · ligand · chains A, B
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 403 | 0.72 | 0.83 | 37 | 031 |
Interfaces
1 interface between chains.
- A–B · 1883 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 3VFA · Crystal Structure of HIV-1 Protease Mutant V82A with novel P1'-Ligands GRL-02031 · 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 P0C6F2
- Elsewhere: RCSB PDB 3VFA · PDBe 3VFA · UniProt P0C6F2
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