Research workbench
Visualizing ATP-dependent RNA translocation by the NS3 helicase from HCV
Analyse Visualizing ATP-dependent RNA translocation by the NS3 helicase from HCV in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3O8R
- Type
- protein + RNA
- Length
- 1,296 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HCV NS3 PROTEASE/HELICASE; RNA (5'-R(P*UP*(5BU)P*UP*UP*UP*U)-3')
- EC
- 3.4.21.98, 3.6.1.15, 3.6.4.13
- UniProt
- Q99AU2
- Ligands
- ADP, BEF, ZN, MG, SO4
- Pockets
- 16 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | HCV NS3 PROTEASE/HELICASE (EC 3.4.21.98, 3.6.1.15, 3.6.4.13) | protein | 645 | 27% helix, 29% strand | Q99AU2 |
| C | RNA (5'-R(P*UP*(5BU)P*UP*UP*UP*U)-3') | rna | 6 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- BEF · Beryllium trifluoride ion · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 995 | 0.80 | 0.82 | 98 | empty |
| 2 | 653 | 0.78 | 0.83 | 68 | SO4 |
| 3 | 240 | 0.70 | 0.86 | 36 | empty |
| 4 | 322 | 0.68 | 0.82 | 51 | empty |
| 5 | 386 | 0.66 | 0.79 | 39 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1342 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1010 Ų buried · 16 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3O8R · Visualizing ATP-dependent RNA Translocation by the NS3 Helicase from HCV · 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 Q99AU2
- Elsewhere: RCSB PDB 3O8R · PDBe 3O8R · UniProt Q99AU2
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