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Crystal structure of inactive HIV-1 protease variant (I50V/A71V) in complex with P1-P6 substrate variant (R452S)
Analyse Crystal structure of inactive HIV-1 protease variant (I50V/A71V) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QJ7
- Type
- protein
- Length
- 414 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease; P1-P6 peptide
- EC
- 3.4.23.16
- UniProt
- P03369
- Ligands
- SO4, PO4
- Pockets
- 2 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 3% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Protease (EC 3.4.23.16) | protein | 99 | 4% helix, 55% strand | P03369 |
| F | P1-P6 peptide | protein | 8 | 0% helix, 38% strand | — |
| G | P1-P6 peptide | protein | 10 | 0% helix, 30% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 93 | 0.54 | 0.84 | 25 | empty |
| 2 | 75 | 0.30 | 0.73 | 18 | empty |
Interfaces
12 interfaces between chains.
- A–B · 1822 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 1799 Ų buried · 35 hydrogen bonds · protein-protein
- D–G · 561 Ų buried · 15 hydrogen bonds · protein-protein
- B–F · 522 Ų buried · 15 hydrogen bonds · protein-protein
- C–G · 482 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4QJ7 · Crystal structure of inactive HIV-1 protease variant (I50V/A71V) in complex with p1-p6… · 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 P03369
- Elsewhere: RCSB PDB 4QJ7 · PDBe 4QJ7 · UniProt P03369
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