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Yorodumi- PDB-4jy0: Crystal structure of hcv ns5b polymerase in complex with compound 3 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jy0 | ||||||
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Title | Crystal structure of hcv ns5b polymerase in complex with compound 3 | ||||||
Components | Genome polyprotein | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE-TRANSFERASE 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 / 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 / molecular adaptor activity / 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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Coulombe, R. | ||||||
Citation | Journal: To be Published Title: Distinguishing drug binding pockets on proteins by complementary biophysical and biological methods. Authors: Coulombe, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jy0.cif.gz | 235 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jy0.ent.gz | 187.2 KB | Display | PDB format |
PDBx/mmJSON format | 4jy0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jy0_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4jy0_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4jy0_validation.xml.gz | 45.7 KB | Display | |
Data in CIF | 4jy0_validation.cif.gz | 64.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jy/4jy0 ftp://data.pdbj.org/pub/pdb/validation_reports/jy/4jy0 | HTTPS FTP |
-Related structure data
Related structure data | 3mwvS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 64285.637 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 2420-2989 Source method: isolated from a genetically manipulated source Details: PROTEIN CONSTRUCT ID 001 / Source: (gene. exp.) Hepatitis C virus / Strain: IBJ4 / Gene: NS5B / Plasmid: PET29B / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) References: UniProt: O92972, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, hepacivirin, nucleoside-triphosphate phosphatase, RNA helicase, 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: 2.96 Å3/Da / Density % sol: 58.5 % |
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Crystal grow | Temperature: 284 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 100 mM MES, 21% PEGmme 5000, 400 mM Ammonium sulfate, 10% glycerol, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 284K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 15, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→40 Å / Num. all: 165830 / Num. obs: 68870 / % possible obs: 88.1 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 10.86 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 2.09 / Num. unique all: 5706 / % possible all: 74.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3MWV Resolution: 2.2→40 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→40 Å
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Refine LS restraints |
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