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Yorodumi- PDB-6nzv: Crystal structure of HCV NS3/4A protease in complex with compound 12 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nzv | ||||||
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Title | Crystal structure of HCV NS3/4A protease in complex with compound 12 | ||||||
Components | HCV NS3/4A protease | ||||||
Keywords | viral protein/inhibitor / viral protease inhibitor / voxilaprevir / hepatitis C virus / VIRAL PROTEIN / viral protein-inhibitor complex | ||||||
Function / homology | Function and homology information : / 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 / ribonucleoside triphosphate phosphatase activity / lipid droplet ...: / 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 / ribonucleoside triphosphate phosphatase activity / lipid droplet / protein complex oligomerization / monoatomic ion channel activity / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / 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 / ribonucleoprotein complex / induction by virus of host autophagy / serine-type endopeptidase activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-dependent RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / structural molecule activity / host cell plasma membrane / virion membrane / proteolysis / RNA binding / zinc ion binding / ATP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Hepatitis C virus subtype 1a | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Appleby, T.C. / Taylor, J.G. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2019 Title: Discovery of the pan-genotypic hepatitis C virus NS3/4A protease inhibitor voxilaprevir (GS-9857): A component of Vosevi®. Authors: Taylor, J.G. / Zipfel, S. / Ramey, K. / Vivian, R. / Schrier, A. / Karki, K.K. / Katana, A. / Kato, D. / Kobayashi, T. / Martinez, R. / Sangi, M. / Siegel, D. / Tran, C.V. / Yang, Z.Y. / ...Authors: Taylor, J.G. / Zipfel, S. / Ramey, K. / Vivian, R. / Schrier, A. / Karki, K.K. / Katana, A. / Kato, D. / Kobayashi, T. / Martinez, R. / Sangi, M. / Siegel, D. / Tran, C.V. / Yang, Z.Y. / Zablocki, J. / Yang, C.Y. / Wang, Y. / Wang, K. / Chan, K. / Barauskas, O. / Cheng, G. / Jin, D. / Schultz, B.E. / Appleby, T. / Villasenor, A.G. / Link, J.O. #1: Journal: Bioorg.Med.Chem.Lett. / Year: 2019 Title: Discovery of velpatasvir (GS-5816): A potent pan-genotypic HCV NS5A inhibitor in the single-tablet regimens Vosevi®and Epclusa®. Authors: Link, J.O. / Taylor, J.G. / Trejo-Martin, A. / Kato, D. / Katana, A.A. / Krygowski, E.S. / Yang, Z.Y. / Zipfel, S. / Cottell, J.J. / Bacon, E.M. / Tran, C.V. / Yang, C.Y. / Wang, Y. / Wang, ...Authors: Link, J.O. / Taylor, J.G. / Trejo-Martin, A. / Kato, D. / Katana, A.A. / Krygowski, E.S. / Yang, Z.Y. / Zipfel, S. / Cottell, J.J. / Bacon, E.M. / Tran, C.V. / Yang, C.Y. / Wang, Y. / Wang, K.W. / Zhao, G. / Cheng, G. / Tian, Y. / Gong, R. / Lee, Y.J. / Yu, M. / Gorman, E. / Mogalian, E. / Perry, J.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nzv.cif.gz | 58.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nzv.ent.gz | 38.3 KB | Display | PDB format |
PDBx/mmJSON format | 6nzv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nz/6nzv ftp://data.pdbj.org/pub/pdb/validation_reports/nz/6nzv | HTTPS FTP |
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-Related structure data
Related structure data | 6nztC 3m5lS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21516.371 Da / Num. of mol.: 1 / Mutation: D168Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis C virus subtype 1a / Production host: Escherichia coli (E. coli) / References: UniProt: S4UY05 |
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#2: Chemical | ChemComp-L9J / ( |
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 8-10% PEG 3350, 0.1M ammonium sulfate, 0.1M MES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.976 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 6, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. obs: 151435 / % possible obs: 99.9 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 25.05 |
Reflection shell | Resolution: 1.55→1.59 Å / Rmerge(I) obs: 0.379 / Num. measured obs: 2059 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3M5L Resolution: 1.55→42.028 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 16.88
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→42.028 Å
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Refine LS restraints |
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LS refinement shell |
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