MolNFT v1 · #15334 · protein
Crystal structure of HCV NS3 protease DOMAIN:NS4A peptide complex with covalently bound inhibitor (GW472467X)
1N1L · HCV NS3 serine protease: “Crystal structure of HCV NS3 protease DOMAIN:NS4A peptide complex with covalently bound inhibitor (GW472467X)”. X-ray diffraction, 2 ligands (TRL, ZN), 3 pockets (best druggability 0.59). MolNFT v1 #15334…
- PDB
- 1N1L
- Type
- protein
- Length
- 370 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HCV NS3 serine protease; NS4A cofactor
- UniProt
- P27958
- Ligands
- TRL, ZN
- Pockets
- 3 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HCV NS3 serine protease | protein | 180 | 14% helix, 43% strand | P27958 |
| B | HCV NS3 serine protease | protein | 153 | 10% helix, 50% strand | P27958 |
| C | NS4A cofactor | protein | 21 | 0% helix, 48% strand | — |
| D | NS4A cofactor | protein | 16 | 0% helix, 50% strand | — |
Ligands and binding sites
- TRL · {1-[2-(1-formyl-propyl)-3-methanesulfonylamino-pyrrolidine-1-carbonyl]-2-methyl-propyl}-carbamic acid tert-butyl ester · ligand · chains A
- 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
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 93 | 0.59 | 0.88 | 19 | empty |
| 2 | 92 | 0.35 | 0.75 | 20 | empty |
| 3 | 57 | 0.28 | 0.74 | 16 | TRL |
Interfaces
6 interfaces between chains.
- A–C · 1260 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 843 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 458 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 292 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 208 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1N1L · Crystal structure of HCV NS3 protease DOMAIN:NS4A peptide complex with covalently bound… · 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 P27958
- Elsewhere: RCSB PDB 1N1L · PDBe 1N1L · UniProt P27958
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