MolNFT v1 · #89245 · protein
Crystal structure of wild-type HIV-1 protease in complex with MKP56
4DJO · Pol polyprotein: “Crystal structure of wild-type HIV-1 protease in complex with MKP56”. X-ray diffraction, 2 ligands (MK5, PO4), 1 pocket (best druggability 0.70). MolNFT v1 #89245 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4DJO
- Type
- protein
- Length
- 198 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pol polyprotein
- UniProt
- Q90K99
- Ligands
- MK5, PO4
- Pockets
- 1 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pol polyprotein | protein | 99 | 4% helix, 54% strand | Q90K99 |
Ligands and binding sites
- MK5 · 2-[(dichloroacetyl)amino]ethyl [(2S,3R)-3-hydroxy-4-{[(4-methoxyphenyl)sulfonyl][(2S)-2-methylbutyl]amino}-1-phenylbutan-2-yl]carbamate · ligand · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A, B
- ACT · Acetate ion · additive · chains A
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 | 375 | 0.70 | 0.82 | 36 | MK5 |
Interfaces
1 interface between chains.
- A–B · 1847 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 4DJO · Crystal Structure of wild-type HIV-1 Protease in Complex with MKP56 · 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 Q90K99
- Elsewhere: RCSB PDB 4DJO · PDBe 4DJO · UniProt Q90K99
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