Research workbench
Crystal structure of hepatitis C virus NS5B polymerase from 1B genotype in complex with a non-nucleoside inhibitor
Analyse Crystal structure of hepatitis C virus NS5B polymerase from 1B genotype in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WHO
- Type
- protein
- Length
- 1,062 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase
- EC
- 2.7.7.48
- UniProt
- P26663
- Ligands
- VGI, MN
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 531 | 50% helix, 15% strand | P26663 |
Ligands and binding sites
- VGI · 2-(3-bromophenyl)-6-[(2-hydroxyethyl)amino]-1h-benzo[de]isoquinoline-1,3(2h)-dione · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 493 | 0.72 | 0.81 | 67 | empty |
| 2 | 339 | 0.64 | 0.79 | 44 | empty |
| 3 | 394 | 0.63 | 0.78 | 48 | empty |
| 4 | 224 | 0.59 | 0.80 | 37 | empty |
| 5 | 72 | 0.57 | 0.88 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1356 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 2WHO · Crystal structure of hepatitis C virus NS5B polymerase from 1B genotype in complex with a… · 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 P26663
- Elsewhere: RCSB PDB 2WHO · PDBe 2WHO · UniProt P26663
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