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Yorodumi- PDB-2ax1: Hepatitis C Virus NS5b RNA Polymerase in complex with a covalent ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ax1 | ||||||
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Title | Hepatitis C Virus NS5b RNA Polymerase in complex with a covalent inhibitor (5ee) | ||||||
Components | Genome polyprotein | ||||||
Keywords | TRANSFERASE / HCV / NS5B / Polymerase / Fingers / Thumb / Palm | ||||||
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 / structural molecule activity / host cell plasma membrane / 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 / Rigid-body refinement / Resolution: 2.1 Å | ||||||
Authors | Powers, J.P. / Piper, D.E. / Li, Y. / Mayorga, V. / Anzola, J. / Chen, J.M. / Jaen, J.C. / Lee, G. / Liu, J. / Peterson, M.G. ...Powers, J.P. / Piper, D.E. / Li, Y. / Mayorga, V. / Anzola, J. / Chen, J.M. / Jaen, J.C. / Lee, G. / Liu, J. / Peterson, M.G. / Tonn, G.R. / Ye, Q. / Walker, N.P. / Wang, Z. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2006 Title: SAR and Mode of Action of Novel Non-Nucleoside Inhibitors of Hepatitis C NS5b RNA Polymerase. Authors: Powers, J.P. / Piper, D.E. / Li, Y. / Mayorga, V. / Anzola, J. / Chen, J.M. / Jaen, J.C. / Lee, G. / Liu, J. / Peterson, M.G. / Tonn, G.R. / Ye, Q. / Walker, N.P. / Wang, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ax1.cif.gz | 238.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ax1.ent.gz | 197.2 KB | Display | PDB format |
PDBx/mmJSON format | 2ax1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/2ax1 ftp://data.pdbj.org/pub/pdb/validation_reports/ax/2ax1 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 64638.066 Da / Num. of mol.: 2 / Fragment: NS5B RNA-directed RNA polymerase Mutation: V499A,S506N,Q514R,T520I,P540A,S543G,V552T,S563G,L564V,R566H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis C virus / Genus: Hepacivirus / Production host: Escherichia coli (E. coli) / References: UniProt: P26663, RNA-directed RNA polymerase #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: 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: 2.5 Å3/Da / Density % sol: 50.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 200 mM ammonium sulfate, 27% PEG-5000 MME, 100 mM sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 14, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→40 Å / Num. all: 67507 / Num. obs: 67443 / % possible obs: 93.1 % / Observed criterion σ(I): -3 / Rsym value: 0.058 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.1→2.18 Å / Rsym value: 0.35 / % possible all: 70.7 |
-Processing
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Refinement | Method to determine structure: Rigid-body refinement / Resolution: 2.1→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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