Research workbench
HCV NS3 protease domain with a ketoamide inhibitor covalently bound.
Analyse HCV NS3 protease domain with a ketoamide inhibitor covalently bound. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2A4R
- Type
- protein
- Length
- 370 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NS3 PROTEASE/HELICASE; NS4A peptide
- UniProt
- Q91RS4, O39914
- Ligands
- BNH, ZN
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NS3 PROTEASE/HELICASE | protein | 181 | 14% helix, 46% strand | Q91RS4 |
| B | NS4A peptide | protein | 22 | 0% helix, 45% strand | O39914 |
| C | NS3 PROTEASE/HELICASE | protein | 151 | 10% helix, 51% strand | Q91RS4 |
| D | NS4A peptide | protein | 16 | 0% helix, 56% strand | O39914 |
Ligands and binding sites
- BNH · [(N-{3-[(N-{cyclohexyl[(isobutoxycarbonyl)amino]acetyl}-3-cyclopropylalanyl)amino]-4-cyclopropyl-2-oxobutanoyl}glycyl)amino](phenyl)acetic acid · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A, C
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 | 115 | 0.60 | 0.86 | 26 | empty |
| 2 | 65 | 0.39 | 0.79 | 16 | empty |
| 3 | 99 | 0.38 | 0.76 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1282 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 854 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 455 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 306 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 227 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 2A4R · HCV NS3 Protease Domain with a Ketoamide Inhibitor 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
- Every structure of UniProt O39914
- Elsewhere: RCSB PDB 2A4R · PDBe 2A4R · UniProt Q91RS4 · UniProt O39914
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