Research workbench
Crystal structure of HCV NS3/4A protease complexed with inhibitor
Analyse Crystal structure of HCV NS3/4A protease complexed with inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K8B
- Type
- protein
- Length
- 378 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NS3 protease; Nonstructural protein
- EC
- 3.4.21.98
- UniProt
- Q0ZNA6, Q81584
- Ligands
- 1RR, ZN, SO4
- Pockets
- 2 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NS3 protease (EC 3.4.21.98) | protein | 177 | 14% helix, 47% strand | Q0ZNA6 |
| C, D | Nonstructural protein | protein | 12 | 0% helix, 75% strand | Q81584 |
Ligands and binding sites
- 1RR · N-(tert-butylcarbamoyl)-3-methyl-L-valyl-(4R)-N-[(1R,2S)-1-carboxy-2-ethenylcyclopropyl]-4-[(7-methoxy-2-phenylquinolin-4-yl)oxy]-L-prolinamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 409 | 0.57 | 0.74 | 43 | 1RR |
| 2 | 56 | 0.35 | 0.78 | 14 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1194 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 1192 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 186 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4K8B · Crystal structure of HCV NS3/4A protease complexed with inhibitor · 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 Q0ZNA6
- Every structure of UniProt Q81584
- Elsewhere: RCSB PDB 4K8B · PDBe 4K8B · UniProt Q0ZNA6 · UniProt Q81584
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