› 5qj0

X-ray diffraction
2.08Å resolution

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

Released:
DOI: 10.2210/pdb5qj0/pdb
PDB entry 5qj0 coloured by chain, front view.
PDB entry 5qj0 coloured by chain, side view.
PDB entry 5qj0 coloured by chain, top view.
Source organism: Hepacivirus hominis
Primary publication:
Structure-Property Basis for Solving Transporter-Mediated Efflux and Pan-Genotypic Inhibition in HCV NS5B Inhibitors.
Yeung KS, Beno BR, Mosure K, Zhu J, Grant-Young KA, Parcella K, Anjanappa P, Bora RO, Selvakumar K, Wang YK, Fang H, Krause R, Rigat K, Liu M, Lemm J, Sheriff S, Witmer M, Tredup J, Jardel A, Kish K, Parker D, Haskell R, Santone K, Meanwell NA, Soars MG, Roberts SB, Kadow JF
ACS Med Chem Lett 9 1217-1222 (2018)
PMID: 30613329

Function and Biology Details

Reactions catalysed: 
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Hydrolysis of four peptide bonds in the viral precursor polyprotein, commonly with Asp or Glu in the P6 position, Cys or Thr in P1 and Ser or Ala in P1'.
NTP + H(2)O = NDP + phosphate
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-189307 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
RNA-directed RNA polymerase Chain: A
Molecule details ›
Chain: A
Length: 574 amino acids
Theoretical weight: 63.93 KDa
Source organism: Hepacivirus hominis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q99IB8 (Residues: 2443-3015; Coverage: 19%)
Sequence domains: Viral RNA dependent RNA polymerase

Ligands and Environments

4 bound ligands:
Ligand J6D 1 x J6D
Ligand SCN 3 x SCN
Ligand 2PE 1 x 2PE
Ligand GOL 5 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CLSI BEAMLINE 08ID-1
Spacegroup: P212121
Unit cell:
a: 62.25Å b: 89.986Å c: 124.09Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.174 0.173 0.21
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 mentions without citation

Revisiting Viral RNA-Dependent RNA Polymerases: Insights from Recent Structural Studies.
Ramaswamy et al. (2022)
1 more