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Crystal structure of the hepatitis C virus NS5B RNA-dependent RNA polymerase complex with BMS-791325 also known as (1aR,12bS)-8-cyclohexyl-n-(dimethylsulfamoyl)-11-methoxy-1a-{[(1R,5S)-3-methyl-3,8-diazabicyclo[3.2.1]oct-8-yl]carbonyl}-1,1a,2,12b-tetrahydrocyclopropa[d]indolo[2,1-a][2]benzazepine-5-carboxamide and 2-(4-fluorophenyl)-n-methyl-6-[(methylsulfonyl)amino]-5-(propan-2-yloxy)-1-benzofuran-3-carboxamide

Source organism: Hepatitis C virus (isolate Con1)
Biochemical function: RNA-dependent RNA polymerase activity
Biological process: viral RNA genome replication
Cellular component: not assigned

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EC 3.6.4.13: RNA helicase

Reaction catalysed:
ATP + H(2)O = ADP + phosphate
Systematic name:
ATP phosphohydrolase (RNA helix unwinding)
Alternative Name(s):
  • CSFV NS3 helicase
  • DBP2
  • DDX17
  • DDX25
  • DDX3
  • DDX3X
  • DDX3Y
  • DDX4
  • DDX5
  • DEAD-box RNA helicase
  • DEAD-box protein DED1
  • DEAH-box RNA helicase
  • DEAH-box protein 2
  • DED1
  • DbpA
  • Dex(H/D) RNA helicase
  • EIF4A helicase
  • EhDEAD1
  • EhDEAD1 RNA helicase
  • GRTH/DDX25
  • KOKV helicase
  • Mtr4p
  • NPH-II
  • Nonstructural protein 3 helicase
  • RHA
  • RNA helicase A
  • RNA helicase DDX3
  • RNA helicase Hera
  • RNA-dependent ATPase
  • TGBp1 NTPase/helicase domain
  • VRH1

EC 3.6.1.15: Nucleoside-triphosphate phosphatase

Reaction catalysed:
NTP + H(2)O = NDP + phosphate
Systematic name:
Unspecific diphosphate phosphohydrolase
Alternative Name(s):
  • NTPase
  • Nucleoside 5-triphosphatase
  • Nucleoside triphosphate hydrolase
  • Nucleoside triphosphate phosphohydrolase
  • Nucleoside-5-triphosphate phosphohydrolase
  • Nucleoside-triphosphatase

EC 3.4.21.98: Hepacivirin

Reaction catalysed:
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'.
Alternative Name(s):
  • Cpro-2
  • Hepatitis C virus NS3 serine proteinase
  • NS3-4A serine proteinase complex

EC 2.7.7.48: RNA-directed RNA polymerase

Reaction catalysed:
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Systematic name:
Nucleoside-triphosphate:RNA nucleotidyltransferase (RNA-directed)
Alternative Name(s):
  • 3D polymerase
  • PB1 proteins
  • PB2 proteins
  • Phage f2 replicase
  • Polymerase L
  • Q-beta replicase
  • RDRP
  • RNA nucleotidyltransferase (RNA-directed)
  • RNA replicase
  • RNA synthetase
  • RNA transcriptase
  • RNA-dependent RNA polymerase
  • RNA-dependent RNA replicase
  • RNA-dependent ribonucleate nucleotidyltransferase
  • Ribonucleic acid replicase
  • Ribonucleic acid-dependent ribonucleate nucleotidyltransferase
  • Ribonucleic acid-dependent ribonucleic acid polymerase
  • Ribonucleic replicase
  • Ribonucleic synthetase
  • Transcriptase

GO terms

Biochemical function:
Biological process:
Cellular component:
  • not assigned

Sequence family

Pfam Protein family (Pfam)
PF00998
Domain description: Viral RNA dependent RNA polymerase
Occurring in:
  1. RNA-directed RNA polymerase
The deposited structure of PDB entry 4nld contains 1 copy of Pfam domain PF00998 (Viral RNA dependent RNA polymerase) in RNA-directed RNA polymerase. Showing 1 copy in chain A.

InterPro InterPro annotations
IPR043128
Domain description: Reverse transcriptase/Diguanylate cyclase domain
Occurring in:
  1. RNA-directed RNA polymerase
IPR007094
Domain description: RNA-directed RNA polymerase, catalytic domain
Occurring in:
  1. RNA-directed RNA polymerase
IPR002166
Domain description: RNA dependent RNA polymerase, hepatitis C virus
Occurring in:
  1. RNA-directed RNA polymerase
IPR043502
Domain description: DNA/RNA polymerase superfamily
Occurring in:
  1. RNA-directed RNA polymerase

Structure domain

CATH CATH domain
3.30.70.270
Class: Alpha Beta
Architecture: 2-Layer Sandwich
Topology: Alpha-Beta Plaits
Homology: Alpha-Beta Plaits
Occurring in:
  1. RNA-directed RNA polymerase
The deposited structure of PDB entry 4nld contains 1 copy of CATH domain 3.30.70.270 (Alpha-Beta Plaits) in RNA-directed RNA polymerase. Showing 1 copy in chain A.

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