[English] 日本語
Yorodumi- PDB-1z4u: hepatitis C virus NS5B RNA-dependent RNA polymerase complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1z4u | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | hepatitis C virus NS5B RNA-dependent RNA polymerase complex with inhibitor PHA-00799585 | |||||||||
Components | HCV NS5B POLYMERASE | |||||||||
Keywords | TRANSFERASE / NS5B / polymerase / HCV / fingers / palm / thumb | |||||||||
Function / homology | Function and homology information 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 / host cell mitochondrion / 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 ...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 / host cell mitochondrion / 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 / 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 / symbiont entry into host cell / induction by virus of host autophagy / serine-type endopeptidase activity / cysteine-type endopeptidase activity / 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 / proteolysis / RNA binding / zinc ion binding / ATP binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Hepatitis C virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Pfefferkorn, J.A. / Greene, M. / Nugent, R. / Gross, R.J. / Mitchell, M.A. / Finzel, B.C. / Harris, M.S. / Wells, P.A. / Shelly, J.A. / Anstadt, R. | |||||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2005 Title: Inhibitors of HCV NS5B polymerase. Part 2: Evaluation of the northern region of (2Z)-2-benzoylamino-3-(4-phenoxy-phenyl)-acrylic acid Authors: Pfefferkorn, J.A. / Nugent, R. / Gross, R.J. / Greene, M. / Mitchell, M.A. / Reding, M.T. / Funk, L.A. / Anderson, R. / Wells, P.A. / Shelly, J.A. / Anstadt, R. / Finzel, B.C. / Harris, M.S. ...Authors: Pfefferkorn, J.A. / Nugent, R. / Gross, R.J. / Greene, M. / Mitchell, M.A. / Reding, M.T. / Funk, L.A. / Anderson, R. / Wells, P.A. / Shelly, J.A. / Anstadt, R. / Finzel, B.C. / Harris, M.S. / Kilkuskie, R.E. / Kopta, L.A. / Schwende, F.J. #1: Journal: Bioorg.Med.Chem.Lett. / Year: 2005 Title: Inhibitors of HCV NS5B polymerase: Part 1: Evaluation of the southern region of (2Z)-2-(benzoylamino)-3-(5-phenyl-2-furyl)acrylic acid Authors: Pfefferkorn, J.A. / Greene, M.L. / Nugent, R.A. / Gross, R.J. / Mitchell, M.A. / Finzel, B.C. / Harris, M.S. / Wells, P.A. / Shelly, J.A. / Anstadt, R.A. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1z4u.cif.gz | 126 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1z4u.ent.gz | 97.1 KB | Display | PDB format |
PDBx/mmJSON format | 1z4u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1z4u_validation.pdf.gz | 806.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1z4u_full_validation.pdf.gz | 825.9 KB | Display | |
Data in XML | 1z4u_validation.xml.gz | 26.6 KB | Display | |
Data in CIF | 1z4u_validation.cif.gz | 36.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z4/1z4u ftp://data.pdbj.org/pub/pdb/validation_reports/z4/1z4u | HTTPS FTP |
-Related structure data
Related structure data | 1yvfS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 64382.059 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis C virus / Genus: Hepacivirus / Strain: J1 / Production host: Escherichia coli (E. coli) / References: UniProt: O93077, RNA-directed RNA polymerase |
---|
-Non-polymers , 5 types, 164 molecules
#2: Chemical | ChemComp-CL / | ||
---|---|---|---|
#3: Chemical | ChemComp-PO4 / | ||
#4: Chemical | ChemComp-PH9 / ( | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.54 Å3/Da / Density % sol: 65.23 % |
---|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 25, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 23010 / % possible obs: 92.8 % / Rmerge(I) obs: 0.076 |
Reflection shell | Resolution: 2.8→2.9 Å / Rmerge(I) obs: 0.471 / % possible all: 98 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YVF Resolution: 2.8→30 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→30 Å
|