Research workbench
Crystal structure of the hepatitis C virus genotype 2A strain JFH1 NS5B RNA-dependent RNA polymerase in complex with 6- [ETHYL(METHYLSULFONYL)AMINO]-2-(4-fluorophenyl)-N-methyl-5-(3-{[1- (pyrimidin-2-YL)CYCLOPROPYL]CARBAMOYL}PHENYL)-1-benzofuran-3- carboxamide
Analyse Crystal structure of the hepatitis C virus genotype 2A strain JFH1 NS5B… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5QJ0
- Type
- protein
- Length
- 559 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-dependent RNA polymerase
- EC
- 2.7.7.48
- UniProt
- R9THT8
- Ligands
- J6D, SCN
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-dependent RNA polymerase (EC 2.7.7.48) | protein | 559 | 49% helix, 15% strand | R9THT8 |
Ligands and binding sites
- J6D · 6-[ethyl(methylsulfonyl)amino]-2-(4-fluorophenyl)-N-methyl-5-(3-{[1-(pyrimidin-2-yl) cyclopropyl]carbamoyl}phenyl)-1-benzofuran-3-carboxamide · ligand · chains A
- SCN · Thiocyanate ion · ion · 3 copies · chains A
- GOL · Glycerol · additive · 5 copies · chains A
- 2PE · Nonaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 991 | 0.84 | 0.84 | 94 | J6D, SCN, GOL |
| 2 | 97 | 0.57 | 0.85 | 17 | GOL |
| 3 | 163 | 0.48 | 0.77 | 30 | empty |
| 4 | 56 | 0.41 | 0.81 | 16 | empty |
| 5 | 87 | 0.34 | 0.74 | 20 | empty |
Compared structures
- 5QJ0 · CRYSTAL STRUCTURE OF THE HEPATITIS C VIRUS GENOTYPE 2A STRAIN JFH1 NS5B RNA-DEPENDENT RNA… · 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 R9THT8
- Elsewhere: RCSB PDB 5QJ0 · PDBe 5QJ0 · UniProt R9THT8
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