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Yorodumi- PDB-3fqk: Hepatitis C virus polymerase NS5B (BK 1-570) with HCV-796 inhibitor -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fqk | ||||||
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Title | Hepatitis C virus polymerase NS5B (BK 1-570) with HCV-796 inhibitor | ||||||
Components | RNA-directed RNA polymerase | ||||||
Keywords | TRANSFERASE / HCV / HEPATITIS / NS5B / RNA-DEPENDENT RNA POLYMERASE / HCV-796 | ||||||
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 / serine-type endopeptidase activity / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane Similarity search - Function | ||||||
Biological species | Hepatitis C virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Harris, S.F. / Wong, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Slow binding inhibition and mechanism of resistance of non-nucleoside polymerase inhibitors of hepatitis C virus. Authors: Hang, J.Q. / Yang, Y. / Harris, S.F. / Leveque, V. / Whittington, H.J. / Rajyaguru, S. / Ao-Ieong, G. / McCown, M.F. / Wong, A. / Giannetti, A.M. / Le Pogam, S. / Talamas, F. / Cammack, N. / ...Authors: Hang, J.Q. / Yang, Y. / Harris, S.F. / Leveque, V. / Whittington, H.J. / Rajyaguru, S. / Ao-Ieong, G. / McCown, M.F. / Wong, A. / Giannetti, A.M. / Le Pogam, S. / Talamas, F. / Cammack, N. / Najera, I. / Klumpp, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fqk.cif.gz | 237.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fqk.ent.gz | 188.9 KB | Display | PDB format |
PDBx/mmJSON format | 3fqk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fqk_validation.pdf.gz | 979.2 KB | Display | wwPDB validaton report |
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Full document | 3fqk_full_validation.pdf.gz | 989.9 KB | Display | |
Data in XML | 3fqk_validation.xml.gz | 45.3 KB | Display | |
Data in CIF | 3fqk_validation.cif.gz | 65.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fq/3fqk ftp://data.pdbj.org/pub/pdb/validation_reports/fq/3fqk | HTTPS FTP |
-Related structure data
Related structure data | 3fqlC 2giqS S: Starting model for refinement C: citing same article (ref.) |
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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: 64176.652 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis C virus / Strain: BK / Gene: POL / Production host: Escherichia coli (E. coli) / References: UniProt: P26663, RNA-directed RNA polymerase #2: Chemical | #3: 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: 2.25 Å3/Da / Density % sol: 45.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.9 Details: 50 mM Na Citrate, 7.5% glycerol, 24% PEG 4000, pH 4.9, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 4, 2008 |
Radiation | Monochromator: DOUBLE CRYSTAL Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 59410 / Num. obs: 55845 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 28.2 Å2 / Rsym value: 13.4 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 5438 / Rsym value: 68.9 / % possible all: 91.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2GIQ Resolution: 2.2→48.91 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.925 / SU B: 7.742 / SU ML: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.376 / ESU R Free: 0.255 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.969 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→48.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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