Research workbench
HCV NS3 protease with NS4A peptide and a covalently bound macrocyclic ketoamide compound.
Analyse HCV NS3 protease with NS4A peptide and a covalently bound macrocyclic ketoamide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2A4Q
- 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
- FNH, ZN
- Pockets
- 3 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NS3 PROTEASE/HELICASE' | protein | 181 | 14% helix, 43% strand | Q91RS4 |
| B | NS4A peptide | protein | 22 | 0% helix, 45% strand | O39914 |
| C | NS3 PROTEASE/HELICASE' | protein | 151 | 11% helix, 51% strand | Q91RS4 |
| D | NS4A peptide | protein | 16 | 0% helix, 56% strand | O39914 |
Ligands and binding sites
- FNH · (2R)-({N-[(3S)-3-({[(3S,6S)-6-cyclohexyl-5,8-dioxo-4,7-diazabicyclo[14.3.1]icosa-1(20),16,18-trien-3-yl]carbonyl}amino)-2-oxohexanoyl]glycyl}amino)(phenyl)acetic acid · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A, C
- BME · Beta-mercaptoethanol · additive · chains A
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 | 130 | 0.59 | 0.85 | 25 | empty |
| 2 | 61 | 0.38 | 0.79 | 17 | empty |
| 3 | 57 | 0.31 | 0.76 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1308 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 868 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 455 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 315 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 208 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct, covalent ligand).
Compared structures
- 2A4Q · HCV NS3 protease with NS4a peptide and a covalently bound macrocyclic ketoamide compound. · 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 2A4Q · PDBe 2A4Q · UniProt Q91RS4 · UniProt O39914
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.