+Open data
-Basic information
Entry | Database: PDB / ID: 2hwh | ||||||
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Title | HCV NS5B allosteric inhibitor complex | ||||||
Components | RNA-directed RNA polymerase (NS5B) (p68) | ||||||
Keywords | TRANSFERASE / HCV / NS5B / Viral RNA-directed RNA Polymerase / RdRP / allosteric inhibitor / HCV 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Yao, N. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2006 Title: Structure-based design of a novel thiazolone scaffold as HCV NS5B polymerase allosteric inhibitors. Authors: Yan, S. / Appleby, T. / Larson, G. / Wu, J.Z. / Hamatake, R. / Hong, Z. / Yao, N. | ||||||
History |
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Remark 999 | Sequence According to author, these are due to viral strand differences |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hwh.cif.gz | 226.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hwh.ent.gz | 181.7 KB | Display | PDB format |
PDBx/mmJSON format | 2hwh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hw/2hwh ftp://data.pdbj.org/pub/pdb/validation_reports/hw/2hwh | HTTPS FTP |
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-Related structure data
Related structure data | 2hwiC 1c2pS S: Starting model for refinement C: citing same article (ref.) |
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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: 64013.324 Da / Num. of mol.: 2 / Fragment: HCV NS5B 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 | #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: 2.23 Å3/Da / Density % sol: 44.84 % |
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Crystal grow | Temperature: 295 K / Method: evaporation / pH: 5 Details: 20% PEG 4000, 5 mM DTT, 0.5M MES, 1.0 M NACL, pH 5, MICRO BATCH, pH 5.0, EVAPORATION, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 2, 2003 / Details: Osmic Blue Mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. all: 51621 / Num. obs: 51206 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.3→2.38 Å / Mean I/σ(I) obs: 4.1 / Rsym value: 0.3 / % possible all: 0.993 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry: 1C2P Resolution: 2.3→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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