› 3cj3

X-ray diffraction
1.87Å resolution

Crystal structure of hepatitis c virus rna-dependent rna polymerase ns5b in complex with optimized small molecule fragments

Released:
DOI: 10.2210/pdb3cj3/pdb
PDB entry 3cj3 coloured by chain, front view.
PDB entry 3cj3 coloured by chain, side view.
PDB entry 3cj3 coloured by chain, top view.
Source organism: Hepatitis C virus subtype 1b
Primary publication:
Fragment-based discovery of hepatitis C virus NS5b RNA polymerase inhibitors.
Antonysamy SS, Aubol B, Blaney J, Browner MF, Giannetti AM, Harris SF, Hébert N, Hendle J, Hopkins S, Jefferson E, Kissinger C, Leveque V, Marciano D, McGee E, Nájera I, Nolan B, Tomimoto M, Torres E, Wright T
Bioorg Med Chem Lett 18 2990-5 (2008)
PMID: 18400495

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-150808 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
RNA-directed RNA polymerase Chains: A, B
Molecule details ›
Chains: A, B
Length: 576 amino acids
Theoretical weight: 64.18 KDa
Source organism: Hepatitis C virus subtype 1b
Expression system: Escherichia coli
UniProt:
  • Canonical: P26663 (Residues: 2421-2989; Coverage: 19%)
Sequence domains: Viral RNA dependent RNA polymerase
Structure domains: Alpha-Beta Plaits

Ligands and Environments

2 bound ligands:
Ligand NI 2 x NI
Ligand SX4 2 x SX4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 31-ID
Spacegroup: P212121
Unit cell:
a: 85.972Å b: 105.737Å c: 126.71Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.221 0.218 0.268
Expression system: Escherichia coli

Quick links

Citations

9 review citations

Strategies for development of Dengue virus inhibitors.
Noble et al. (2010)
8 more

2 mentions without citation

RNA Dependent RNA Polymerases: Insights from Structure, Function and Evolution.
Venkataraman et al. (2018)
1 more