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
- 3KQL
- Type
- protein + DNA
- Length
- 886 residues
- Chains
- 4
- 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
- ALF, ADP, MG
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 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, F | 5'-D(*TP*TP*TP*TP*TP*T)-3' | dna | 6 | — | — |
Ligands and binding sites
- ALF · Tetrafluoroaluminate ion · ligand · 2 copies · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 413 | 0.79 | 0.88 | 53 | empty |
| 2 | 1057 | 0.78 | 0.80 | 82 | empty |
| 3 | 287 | 0.59 | 0.78 | 43 | ALF, ADP, MG |
| 4 | 246 | 0.59 | 0.79 | 33 | ALF, ADP, MG |
| 5 | 242 | 0.53 | 0.76 | 22 | empty |
Interfaces
3 interfaces between chains.
- B–F · 996 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–E · 994 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–B · 436 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3KQL · 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 3KQL · PDBe 3KQL · UniProt Q9WMX2
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