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- PDB-6w4g: Hepatitis C virus polymerase NS5B with RO inhibitor for SAR studies -

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Basic information

Entry
Database: PDB / ID: 6w4g
TitleHepatitis C virus polymerase NS5B with RO inhibitor for SAR studies
ComponentsNS5B
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / HCV POL / NS5B / polymerase / TRANSFERASE-TRANSFERASE INHIBITOR / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / SH3 domain binding / nucleoside-triphosphate phosphatase ...hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / SH3 domain binding / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / ribonucleoprotein complex / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
: / Hepatitis C virus core protein, chain A superfamily / Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal ...: / Hepatitis C virus core protein, chain A superfamily / Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus non-structural protein NS4b / Hepatitis C virus capsid protein / Hepatitis C virus, Non-structural protein NS2 / Hepatitis C virus, Non-structural 5a protein / Hepatitis C virus, Non-structural 5a protein, domain 1a / Hepatitis C virus non-structural 5a, 1B domain / NS5A domain 1a superfamily / Hepatitis C virus non-structural 5a protein membrane anchor / Hepatitis C virus non-structural 5a zinc finger domain / Hepatitis C virus non-structural 5a domain 1b / Hepacivirus nonstructural protein 2 (NS2) protease domain profile. / Hepatitis C virus, Non-structural protein NS4a / Hepatitis C virus non-structural protein NS4a / Hepatitis C virus, Core protein, C-terminal / Hepatitis C virus core protein / Hepatitis C virus, Non-structural protein E2/NS1 / Hepatitis C virus non-structural protein E2/NS1 / Hepatitis C virus, Envelope glycoprotein E1 / Hepatitis C virus envelope glycoprotein E1 / RNA dependent RNA polymerase, hepatitis C virus / Viral RNA dependent RNA polymerase / Hepatitis C virus, NS3 protease, Peptidase S29 / Hepatitis C virus NS3 protease / Hepacivirus/Pegivirus NS3 protease domain profile. / DEAD box, Flavivirus / Flavivirus DEAD domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-SL4 / Genome polyprotein
Similarity search - Component
Biological speciesHepatitis C virus genotype 1b
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsHarris, S.F.
CitationJournal: J.Chem.Inf.Model. / Year: 2020
Title: Identification of Noncompetitive Protein-Ligand Interactions for Structural Optimization.
Authors: Tosstorff, A. / Cole, J.C. / Taylor, R. / Harris, S.F. / Kuhn, B.
History
DepositionMar 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NS5B
B: NS5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,4064
Polymers126,4992
Non-polymers9072
Water7,278404
1
A: NS5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7032
Polymers63,2501
Non-polymers4531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NS5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7032
Polymers63,2501
Non-polymers4531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.478, 104.704, 126.119
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NS5B / Nonstructural protein 5B


Mass: 63249.555 Da / Num. of mol.: 2 / Fragment: UNP residues 2421-2981
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus genotype 1b (isolate BK)
Strain: isolate BK / Production host: Escherichia coli (E. coli) / References: UniProt: P26663, RNA-directed RNA polymerase
#2: Chemical ChemComp-SL4 / 5-[[(2~{S})-4-[1,1-bis(oxidanylidene)-1,2-benzothiazol-3-yl]-2-~{tert}-butyl-3-oxidanyl-5-oxidanylidene-2~{H}-pyrrol-1-yl]methyl]-2-fluoranyl-benzenecarbonitrile


Mass: 453.486 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H20FN3O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 50 mm sodium citrate, pH 4.9, 26% PEG4000, 7.5% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 21, 2005
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 61531 / % possible obs: 74 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.075 / Χ2: 1.139 / Net I/σ(I): 12.1 / Num. measured all: 315040
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.95-2.022.70.50719961.044124.3
2.02-2.13.40.43730951.123137.7
2.1-2.23.80.34941531.19150.6
2.2-2.314.10.31851231.187162.2
2.31-2.464.40.2662001.198175.3
2.46-2.654.80.22174481.216190.1
2.65-2.915.70.16581911.219198.8
2.91-3.336.10.10483221.112199.9
3.33-4.26.10.06384011.111199.8
4.2-505.90.03486021.022198.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2GIQ

2giq


Resolution: 1.95→45.64 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.943 / SU B: 6.892 / SU ML: 0.174 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.263 / ESU R Free: 0.215
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2467 3066 5 %RANDOM
Rwork0.1841 ---
obs0.1873 58402 74.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 132.88 Å2 / Biso mean: 44.621 Å2 / Biso min: 24.62 Å2
Baniso -1Baniso -2Baniso -3
1--1.17 Å20 Å20 Å2
2--3.03 Å20 Å2
3----1.85 Å2
Refinement stepCycle: final / Resolution: 1.95→45.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8612 0 64 404 9080
Biso mean--51.3 45.96 -
Num. residues----1104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0138997
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178344
X-RAY DIFFRACTIONr_angle_refined_deg1.6481.65612245
X-RAY DIFFRACTIONr_angle_other_deg1.2931.57319348
X-RAY DIFFRACTIONr_dihedral_angle_1_deg18.8515.2921163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.07320.757423
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.639151511
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6941570
X-RAY DIFFRACTIONr_chiral_restr0.0730.21184
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0210944
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021919
LS refinement shellResolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 74 -
Rwork0.379 1277 -
all-1351 -
obs--22.35 %

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