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Yorodumi- PDB-3hky: HCV NS5B polymerase genotype 1b in complex with 1,5 benzodiazepine 6 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hky | ||||||
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Title | HCV NS5B polymerase genotype 1b in complex with 1,5 benzodiazepine 6 | ||||||
Components | RNA-directed RNA polymeraseRNA-dependent RNA polymerase | ||||||
Keywords | TRANSFERASE / HEPATITIS C VIRUS / 1 / 5-BENZODIAZEPINE / genotype / NS5B / polymerase / Biacore / replicon | ||||||
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 / molecular adaptor 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 / virus-mediated perturbation of host defense response / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane Similarity search - Function | ||||||
Biological species | Hepatitis C virus subtype 1b | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Nyanguile, O. / De Bondt, H.L. | ||||||
Citation | Journal: J.Virol. / Year: 2010 Title: 1a/1b subtype profiling of nonnucleoside polymerase inhibitors of hepatitis C virus Authors: Nyanguile, O. / Devogelaere, B. / Vijgen, L. / Van den Broeck, W. / Pauwels, F. / Cummings, M.D. / De Bondt, H.L. / Vos, A.M. / Berke, J.M. / Lenz, O. / Vandercruyssen, G. / Vermeiren, K. / ...Authors: Nyanguile, O. / Devogelaere, B. / Vijgen, L. / Van den Broeck, W. / Pauwels, F. / Cummings, M.D. / De Bondt, H.L. / Vos, A.M. / Berke, J.M. / Lenz, O. / Vandercruyssen, G. / Vermeiren, K. / Mostmans, W. / Dehertogh, P. / Delouvroy, F. / Vendeville, S. / VanDyck, K. / Dockx, K. / Cleiren, E. / Raboisson, P. / Simmen, K.A. / Fanning, G.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hky.cif.gz | 246.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hky.ent.gz | 196 KB | Display | PDB format |
PDBx/mmJSON format | 3hky.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hk/3hky ftp://data.pdbj.org/pub/pdb/validation_reports/hk/3hky | HTTPS FTP |
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-Related structure data
Related structure data | 3hkwC 1nb4S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 64817.262 Da / Num. of mol.: 2 / Fragment: RESIDUES in UNP 2420-2989 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis C virus subtype 1b / Strain: strain HC-J4 / Gene: NS5B / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O92972, RNA-directed RNA polymerase #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.75 Details: 5-8% PEG 6000, 100mM Mg-Salts, pH 6.75, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0073 / Wavelength: 1.0073 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0073 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→44.9 Å / Num. all: 120846 / Num. obs: 120846 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.086 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.18 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NB4 Resolution: 1.9→44.9 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 7.882 / SU ML: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.899 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→44.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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