Research workbench
Crystal structure of HCV NS3 protease domain: NS4A peptide complex with covalently bound pyrrolidine-5,5-translactam inhibitor
Analyse Crystal structure of HCV NS3 protease domain: NS4A peptide complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RTL
- Type
- protein
- Length
- 370 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NS3 PROTEASE/HELICASE; NS4A cofactor
- UniProt
- Q91RS4
- Ligands
- CPX, ZN
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NS3 PROTEASE/HELICASE | protein | 180 | 14% helix, 43% strand | Q91RS4 |
| B | NS3 PROTEASE/HELICASE | protein | 153 | 10% helix, 50% strand | Q91RS4 |
| C | NS4A cofactor | protein | 21 | 0% helix, 48% strand | — |
| D | NS4A cofactor | protein | 16 | 0% helix, 50% strand | — |
Ligands and binding sites
- CPX · N-[(2R,3S)-1-((2S)-2-{[(cyclopentylamino)carbonyl]amino}-3-methylbutanoyl)-2-(1-formyl-1-cyclobutyl)pyrrolidinyl]cyclopropanecarboxamide · 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 | 129 | 0.60 | 0.85 | 26 | empty |
| 2 | 104 | 0.38 | 0.75 | 20 | empty |
| 3 | 56 | 0.29 | 0.74 | 16 | CPX |
Interfaces
6 interfaces between chains.
- A–C · 1275 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 837 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 485 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 297 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 204 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1RTL · 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 Q91RS4
- Elsewhere: RCSB PDB 1RTL · PDBe 1RTL · UniProt Q91RS4
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