Research workbench
Crystal structure of HCV NS3 protease with a boronate inhibitor
Analyse Crystal structure of HCV NS3 protease with a boronate inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XCN
- Type
- protein
- Length
- 370 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NS3 protease; NS4A
- UniProt
- Q91RS4, C9WU77
- Ligands
- C8D, MG, ZN
- Pockets
- 2 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NS3 protease | protein | 180 | 14% helix, 43% strand | Q91RS4 |
| B | NS3 protease | protein | 153 | 10% helix, 49% strand | Q91RS4 |
| C | NS4A | protein | 21 | 0% helix, 48% strand | C9WU77 |
| D | NS4A | protein | 16 | 0% helix, 56% strand | C9WU77 |
Ligands and binding sites
- C8D · N-[(cyclopentyloxy)carbonyl]-3-methyl-L-valyl-(4R)-N-{(1R)-3-hydroxy-1-[hydroxy(oxido)boranyl]propyl}-4-(isoquinolin-1-yloxy)-L-prolinamide · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, C, D
- ZN · Zinc 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 198 | 0.61 | 0.82 | 33 | MG |
| 2 | 89 | 0.37 | 0.76 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1286 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 850 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 434 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 289 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 207 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2XCN · Crystal structure of HCV NS3 protease with a boronate 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 Q91RS4
- Every structure of UniProt C9WU77
- Elsewhere: RCSB PDB 2XCN · PDBe 2XCN · UniProt Q91RS4 · UniProt C9WU77
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