Research workbench
Three conformational snapshots of the hepatitis C virus NS3 helicase reveal a ratchet translocation mechanism
Analyse Three conformational snapshots of the hepatitis C virus NS3 helicase reveal a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KQN
- Type
- protein + DNA
- Length
- 443 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine PROTEASE/NTPASE/HELICASE NS3; 5'-D(*TP*TP*TP*TP*TP*T)-3'
- EC
- 3.4.21.98, 3.6.1.15, 3.6.1.-
- UniProt
- Q9WMX2
- Ligands
- BEF, ADP, MN
- Pockets
- 2 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine PROTEASE/NTPASE/HELICASE NS3 (EC 3.4.21.98, 3.6.1.15, 3.6.1.-) | protein | 437 | 34% helix, 21% strand | Q9WMX2 |
| E | 5'-D(*TP*TP*TP*TP*TP*T)-3' | dna | 6 | — | — |
Ligands and binding sites
- BEF · Beryllium trifluoride ion · ligand · chains A
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MN · Manganese (II) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 885 | 0.81 | 0.83 | 69 | empty |
| 2 | 274 | 0.60 | 0.79 | 33 | BEF, ADP, MN |
Interfaces
1 interface between chains.
- A–E · 526 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 3KQN · Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal a Ratchet… · 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 Q9WMX2
- Elsewhere: RCSB PDB 3KQN · PDBe 3KQN · UniProt Q9WMX2
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