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Crystal structure of inactive HIV-1 protease variant (I50V/A71V) in complex with wt P1-P6 substrate
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
- 4QJ2
- Type
- protein
- Length
- 416 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease; P1-P6 peptide
- UniProt
- O38710
- Ligands
- SO4, PO4
- Pockets
- 2 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Protease | protein | 99 | 4% helix, 55% strand | O38710 |
| F, G | P1-P6 peptide | protein | 10 | 0% helix, 30% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains B, C
- PO4 · Phosphate ion · ion · chains C, D, F
- GOL · Glycerol · additive · chains A, B
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 | 379 | 0.58 | 0.75 | 39 | empty |
| 2 | 59 | 0.28 | 0.73 | 13 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1817 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 1798 Ų buried · 37 hydrogen bonds · protein-protein
- B–G · 602 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 602 Ų buried · 10 hydrogen bonds · protein-protein
- A–G · 500 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4QJ2 · Crystal structure of inactive HIV-1 protease variant (I50V/A71V) in complex with WT 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 O38710
- Elsewhere: RCSB PDB 4QJ2 · PDBe 4QJ2 · UniProt O38710
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