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- PDB-3phe: HCV NS5B with a bound quinolone inhibitor -

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Basic information

Entry
Database: PDB / ID: 3phe
TitleHCV NS5B with a bound quinolone inhibitor
ComponentsHCV encoded nonstructural 5B protein
KeywordsTransferase/Transferase Inhibitor / Transferase / Polymerase / RNA / Mitochondrial membrane / Transferase-Transferase Inhibitor complex
Function / homology
Function and homology information


host cell membrane / peptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / fusion of virus membrane with host endosome membrane / ATP hydrolysis activity / proteolysis / RNA binding / membrane
Similarity search - Function
RNA dependent RNA polymerase, hepatitis C virus / Viral RNA dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-C9A / RNA-directed RNA polymerase
Similarity search - Component
Biological speciesHepatitis C virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSomoza, J.R. / To, N. / Lehoux, I.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2011
Title: Quinolones as HCV NS5B polymerase inhibitors.
Authors: Kumar, D.V. / Rai, R. / Brameld, K.A. / Somoza, J.R. / Rajagopalan, R. / Janc, J.W. / Xia, Y.M. / Ton, T.L. / Shaghafi, M.B. / Hu, H. / Lehoux, I. / To, N. / Young, W.B. / Green, M.J.
History
DepositionNov 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HCV encoded nonstructural 5B protein
B: HCV encoded nonstructural 5B protein
C: HCV encoded nonstructural 5B protein
D: HCV encoded nonstructural 5B protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)258,8068
Polymers256,4144
Non-polymers2,3924
Water8,845491
1
A: HCV encoded nonstructural 5B protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7022
Polymers64,1031
Non-polymers5981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HCV encoded nonstructural 5B protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7022
Polymers64,1031
Non-polymers5981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: HCV encoded nonstructural 5B protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7022
Polymers64,1031
Non-polymers5981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: HCV encoded nonstructural 5B protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7022
Polymers64,1031
Non-polymers5981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.751, 101.972, 251.087
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
HCV encoded nonstructural 5B protein


Mass: 64103.465 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus / Production host: Escherichia coli (E. coli) / References: UniProt: D0PY27
#2: Chemical
ChemComp-C9A / 4-chlorobenzyl 6-fluoro-7-(4-methylpiperazin-1-yl)-1-[4-(methylsulfonyl)benzyl]-4-oxo-1,4-dihydroquinoline-3-carboxylate


Mass: 598.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C30H29ClFN3O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 491 / Source method: isolated from a natural source / Formula: H2O

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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: 2.54 Å3/Da / Density % sol: 51.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5.1
Details: 16% PEG 4K, 10% glycerol, 5 mM beta-mercaptoethanol, 0.3 M NaCl, 0.1 M NaAcetate, pH 5.1, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 7, 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: 2.2→50 Å / Num. all: 129621 / Num. obs: 129621 / % possible obs: 97.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 2.2→2.24 Å / % possible all: 86.6

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Processing

Software
NameVersionClassification
BOSdata collection
EPMRphasing
CNX2005refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.264 11761 Random
Rwork0.219 --
all0.223 117975 -
obs0.223 117975 -
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17360 0 164 491 18015
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.05
X-RAY DIFFRACTIONx_angle_deg0.743

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