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Yorodumi- PDB-5voj: Crystal structure of HCV NS3/4A protease in complex with JZ01-15,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5voj | |||||||||
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Title | Crystal structure of HCV NS3/4A protease in complex with JZ01-15, an analogue of 5172-mcP1P3 | |||||||||
Components | NS4A cofactor -- NS3 protein chimera | |||||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / NS3/4a Protease / Hepatitis C virus / Drug Resistance / protease inhibitor / HYDROLASE-HYDROLASE 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 / ribonucleoside triphosphate phosphatase activity / lipid droplet ...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 / ribonucleoside triphosphate phosphatase activity / lipid droplet / 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 / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Hepatitis C virus subtype 1a | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.799 Å | |||||||||
Authors | Matthew, A.N. / Schiffer, C.A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J. Med. Chem. / Year: 2017 Title: Hepatitis C Virus NS3/4A Protease Inhibitors Incorporating Flexible P2 Quinoxalines Target Drug Resistant Viral Variants. Authors: Matthew, A.N. / Zephyr, J. / Hill, C.J. / Jahangir, M. / Newton, A. / Petropoulos, C.J. / Huang, W. / Kurt-Yilmaz, N. / Schiffer, C.A. / Ali, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5voj.cif.gz | 93 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5voj.ent.gz | 68.5 KB | Display | PDB format |
PDBx/mmJSON format | 5voj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5voj_validation.pdf.gz | 817.5 KB | Display | wwPDB validaton report |
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Full document | 5voj_full_validation.pdf.gz | 822.5 KB | Display | |
Data in XML | 5voj_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 5voj_validation.cif.gz | 17.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vo/5voj ftp://data.pdbj.org/pub/pdb/validation_reports/vo/5voj | HTTPS FTP |
-Related structure data
Related structure data | 5vp9C 5epnS 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: 21503.330 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis C virus subtype 1a / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A8DG50, UniProt: P26664*PLUS |
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#2: Chemical | ChemComp-9H4 / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-ZN / |
#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: 2.31 Å3/Da / Density % sol: 46.75 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 100 mM MES BUFFER pH 6.5, 4% (W/V) AMMONIUM SULFATE, 20-26% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Feb 13, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.799→20.95 Å / Num. obs: 17608 / % possible obs: 94.1 % / Redundancy: 6.9 % / Rsym value: 0.05 / Net I/σ(I): 7.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5EPN Resolution: 1.799→20.945 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.08
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.799→20.945 Å
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Refine LS restraints |
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LS refinement shell |
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