MolNFT v1 · #104725 · protein
Crystal structure of inactive HIV-1 protease variant (I50V/A71V) in complex with P1-P6 substrate variant (P453L)
4QJ8: “Crystal structure of inactive HIV-1 protease variant (I50V/A71V) in complex with P1-P6 substrate variant…”. X-ray diffraction, 1 ligand (PO4), 3 pockets (best druggability 0.62). MolNFT v1 #104725 on GenesisL1: 3D structure, binding…
- PDB
- 4QJ8
- Type
- protein
- Length
- 416 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
- PO4
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Protease (EC 3.4.23.16) | protein | 99 | 7% helix, 55% strand | P03369 |
| E, F | P1-P6 peptide | protein | 10 | 0% helix, 30% strand | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, E, C, D, F
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 388 | 0.62 | 0.77 | 36 | PO4 |
| 2 | 190 | 0.45 | 0.74 | 24 | empty |
| 3 | 63 | 0.31 | 0.75 | 16 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1821 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 1820 Ų buried · 33 hydrogen bonds · protein-protein
- C–F · 627 Ų buried · 14 hydrogen bonds · protein-protein
- B–E · 607 Ų buried · 15 hydrogen bonds · protein-protein
- D–F · 520 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4QJ8 · 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 4QJ8 · PDBe 4QJ8 · UniProt P03369
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