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- PDB-4jtw: Crystal structure of HCV NS5B polymerase in complex with coupound 1 -
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Open data
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Basic information
Entry | Database: PDB / ID: 4jtw | ||||||
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Title | Crystal structure of HCV NS5B polymerase in complex with coupound 1 | ||||||
![]() | Genome polyprotein | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / RNA-DIRECTED RNA POLYMERASE / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX | ||||||
Function / homology | ![]() 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 / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Coulombe, R. | ||||||
![]() | ![]() Title: Molecular Dynamics Simulations and Structure-Based Rational Design Lead to Allosteric HCV NS5B Polymerase Thumb Pocket 2 Inhibitor with Picomolar Cellular Replicon Potency. Authors: Hucke, O. / Coulombe, R. / Bonneau, P. / Bertrand-Laperle, M. / Brochu, C. / Gillard, J. / Joly, M.A. / Landry, S. / Lepage, O. / Llinas-Brunet, M. / Pesant, M. / Poirier, M. / Poirier, M. / ...Authors: Hucke, O. / Coulombe, R. / Bonneau, P. / Bertrand-Laperle, M. / Brochu, C. / Gillard, J. / Joly, M.A. / Landry, S. / Lepage, O. / Llinas-Brunet, M. / Pesant, M. / Poirier, M. / Poirier, M. / McKercher, G. / Marquis, M. / Kukolj, G. / Beaulieu, P.L. / Stammers, T.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 234.2 KB | Display | ![]() |
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PDB format | ![]() | 186.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 46.4 KB | Display | |
Data in CIF | ![]() | 64.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4jtyC ![]() 4jtzC ![]() 4ju1C ![]() 4ju2C ![]() 3mwvS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: RNA-DIRECTED RNA POLYMERASE, UNP RESIDUES 2420-2989 Source method: isolated from a genetically manipulated source Details: PROTEIN CONSTRUCT ID 001 / Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O92972, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, hepacivirin, nucleoside-triphosphate phosphatase, RNA helicase, RNA-directed RNA polymerase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.21 % |
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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: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 6, 2009 / Details: hires2 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 3→40 Å / Num. obs: 31347 / % possible obs: 98.1 % / Observed criterion σ(I): 1 / Redundancy: 6.6 % / Rmerge(I) obs: 0.149 / Net I/σ(I): 10.84 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2653 / % possible all: 84.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3MWV Resolution: 3→40 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3→40 Å
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Refine LS restraints |
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