Research workbench
Crystal structure of HCV NS3/NS4A protease complexed with des-bromine analogue of BI 201335
Analyse Crystal structure of HCV NS3/NS4A protease complexed with des-bromine analogue… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3P8O
- Type
- protein
- Length
- 390 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- Hepatitis C virus; SYNTHETIC CONSTRUCT
- Molecule
- HCV serine protease NS3; HCV non-structural protein 4A
- EC
- 3.4.21.98
- UniProt
- P26662
- Ligands
- L5T, NA
- Pockets
- 1 · best druggability 0.38
Structure
x-ray diffraction · resolution 2.3 · 2 distinct chains · 13% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | HCV serine protease NS3 (EC 3.4.21.98) | protein | 182 | 14% helix, 43% strand | P26662 |
| C, D | HCV non-structural protein 4A | protein | 13 | 0% helix, 69% strand | — |
Ligands and binding sites
- L5T · N-[(cyclopentyloxy)carbonyl]-3-methyl-L-valyl-(4R)-N-[(1R,2S)-1-carboxy-2-ethenylcyclopropyl]-4-[(7-methoxy-2-{2-[(2-methylpropanoyl)amino]-1,3-thiazol-4-yl}quinolin-4-yl)oxy]-L-prolinamide · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.38 | 0.80 | 15 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1256 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 1209 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 438 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3P8O · Crystal structure of HCV NS3/NS4A protease complexed with des-bromine analogue of bi… · 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 P26662
- Elsewhere: RCSB PDB 3P8O · PDBe 3P8O · UniProt P26662
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