Research workbench
Crystal structure of HIV-1 protease (Q7K, L33I, L63I) in complex with kni-10265
Analyse Crystal structure of HIV-1 protease (Q7K, L33I, L63I) in complex with kni-10265 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KDD
- 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
- P03367
- Ligands
- JZQ
- Pockets
- 1 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protease (EC 3.4.23.16) | protein | 99 | 4% helix, 56% strand | P03367 |
Ligands and binding sites
- JZQ · (4R)-3-[(2S,3S)-3-{[(2,6-difluorophenoxy)acetyl]amino}-2-hydroxy-4-phenylbutanoyl]-N-[(1S,2R)-2-hydroxy-2,3-dihydro-1H- inden-1-yl]-5,5-dimethyl-1,3-thiazolidine-4-carboxamide · ligand · chains A, B
- GOL · Glycerol · additive · 2 copies · chains 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 | 352 | 0.72 | 0.84 | 41 | JZQ |
Interfaces
1 interface between chains.
- A–B · 1849 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 3KDD · Crystal Structure of HIV-1 Protease (Q7K, L33I, L63I) in Complex with KNI-10265 · 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 P03367
- Elsewhere: RCSB PDB 3KDD · PDBe 3KDD · UniProt P03367
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