3QGI: RNA-directed RNA polymerase

Crystal structure of the hepatitis C virus NS5B RNA-dependent RNA polymerase genotype 1a complex with N-[(2S)-butan-2-yl]-6-[(3R)-3-{[4-(trifluoromethoxy)benzyl]carbamoyl}-4-{[4-(trifluoromethoxy)phenyl]sulfonyl}piperazin-1-yl]pyridazine-3-carboxamide. Determined by X-ray diffraction at 1.8 Å resolution. Released 20 Apr 2011.

Method

X-ray diffraction

Resolution

1.8 Å

Organism

Hepatitis C virus subtype 1a

Chains

1

Atoms

5,008

Mol. weight

65.01 kDa

Ligands

33F

Released

20 Apr 2011

Explore 3QGI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3QGI contains 45 α-helices and 29 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 45 helices, 29 β-strands

Molecules and chains

>3QGI_1 RNA-directed RNA polymerase (chains A)
ASMSYSWTGALVTPCAAEEQKLPINALSNSLLRHHNLVYSTTSRSACQRQKKVTFDRLQV
LDSHYQDVLKEVKAAASKVKANLLSVEEACSLTPPHSAKSKFGYGAKDVRCHARKAVAHI
NSVWKDLLEDSVTPIDTTIMAKNEVFCVQPEKGGRKPARLIVFPDLGVRVCEKMALYDVV
SKLPLAVMGSSYGFQYSPGQRVEFLVQAWKSKKTPMGFSYDTRCFDSTVTESDIRTEEAI
YQCCDLDPQARVAIKSLTERLYVGGPLTNSRGENCGYRRCRASGVLTTSCGNTLTCYIKA
RAACRAAGLQDCTMLVCGDDLVVICESAGVQEDAASLRAFTEAMTRYSAPPGDPPQPEYD
LELITSCSSNVSVAHDGAGKRVYYLTRDPTTPLARAAWETARHTPVNSWLGNIIMFAPTL
WARMILMTHFFSVLIARDQLEQALNCEIYGACYSIEPLDLPPIIQRLHGLSAFSLHSYSP
GEINRVAACLRKLGVPPLRAWRHRARSVRARLLSRGGRAAICGKYLFNWAVRTKLKLTPI
AAAGRLDLSGWFTAGYSGGDIYHSVSHARPR

Ligands and cofactors

Water and common crystallization additives (GOL) are not listed.

Primary citation

Investigation of the mode of binding of a novel series of N-benzyl-4-heteroaryl-1-(phenylsulfonyl)piperazine-2-carboxamides to the hepatitis C virus polymerase. Gentles, R.G., Sheriff, S., Beno, B.R. et al. Bioorg Med Chem Lett (2011) 21:2212-2215. DOI 10.1016/j.bmcl.2011.03.011 · PubMed

Related structures

Other PDB entries of the same protein (UniProt P26664 (AlphaFold model), which also has an AlphaFold model), best resolution first:

• 3RC4 1.5 Å, Molecular mechanisms of viral and host-cell substrate recognition by HCV NS3/4A protease
• 3HKW 1.55 Å, HCV NS5B genotype 1a in complex with 1,5 benzodiazepine inhibitor 6
• 7MME 1.56 Å, Crystal structure of HCV NS3/4A D168A protease in complex with JZ01-15
• 3RC5 1.6 Å, Molecular mechanisms of viral and host-cell substrate recognition by HCV NS3/4A protease
• 7MMA 1.65 Å, Crystal structure of HCV NS3/4A protease in complex with NR01-145
• 7MML 1.7 Å, Crystal structure of HCV NS3/4A D168A protease in complex with NR01-145
• 6P6L 1.73 Å, HCV NS3/4A protease domain of genotype 1a in complex with glecaprevir
• 6P6R 1.75 Å, HCV NS3/4A protease domain of genotype 1a3a chimera in complex with glecaprevir
• 7MM3 1.78 Å, Crystal structure of HCV NS3/4A protease in complex with NR01-127
• 5VOJ 1.8 Å, Crystal structure of HCV NS3/4A protease in complex with JZ01-15, an analogue of…
• 5VP9 1.86 Å, Crystal structure of HCV NS3/4A protease in complex with AM-07, an analogue of 5172-mcP1P3
• 7MM4 1.89 Å, Crystal structure of HCV NS3/4A protease in complex with NR01-115

Browse structure collections

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