Research workbench
Crystal structure of HCV NS3/NS4A protease complexed with bi 201335
Analyse Crystal structure of HCV NS3/NS4A protease complexed with bi 201335 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3P8N
- Type
- protein
- Length
- 390 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HCV serine protease NS3; HCV non-structural protein 4A
- EC
- 3.4.21.98
- UniProt
- P26662
- Ligands
- L4T, NA
- Pockets
- 2 · best druggability 0.37
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | HCV serine protease NS3 (EC 3.4.21.98) | protein | 182 | 17% helix, 45% strand | P26662 |
| C, D | HCV non-structural protein 4A | protein | 13 | 0% helix, 69% strand | — |
Ligands and binding sites
- L4T · N-[(cyclopentyloxy)carbonyl]-3-methyl-L-valyl-(4R)-4-[(8-bromo-7-methoxy-2-{2-[(2-methylpropanoyl)amino]-1,3-thiazol-4-yl}quinolin-4-yl)oxy]-N-[(1R,2S)-1-carboxy-2-ethenylcyclopropyl]-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
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.37 | 0.78 | 19 | empty |
| 2 | 54 | 0.35 | 0.79 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1222 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 1196 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 442 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3P8N · Crystal structure of HCV NS3/NS4A protease complexed with BI 201335 · 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 3P8N · PDBe 3P8N · UniProt P26662
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