+Open data
-Basic information
Entry | Database: PDB / ID: 5jjr | ||||||
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Title | Dengue 3 NS5 protein with compound 29 | ||||||
Components | Genome polyprotein | ||||||
Keywords | TRANSFERASE/INHIBITOR / RdRP / Dengue / TRANSFERASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / viral capsid / : / nucleoside-triphosphate phosphatase / double-stranded RNA binding / protein complex oligomerization ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / viral capsid / : / nucleoside-triphosphate phosphatase / double-stranded RNA binding / protein complex oligomerization / monoatomic ion channel activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / virion attachment to host cell / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Dengue virus 3 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å | ||||||
Authors | Lescar, J. / El Sahili, A. | ||||||
Citation | Journal: Plos Pathog. / Year: 2016 Title: Potent Allosteric Dengue Virus NS5 Polymerase Inhibitors: Mechanism of Action and Resistance Profiling Authors: Lim, S.P. / Noble, C.G. / Seh, C.C. / Soh, T.S. / El Sahili, A. / Chan, G.K. / Lescar, J. / Arora, R. / Benson, T. / Nilar, S. / Manjunatha, U. / Wan, K.F. / Dong, H. / Xie, X. / Shi, P.Y. / Yokokawa, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jjr.cif.gz | 202.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jjr.ent.gz | 155.9 KB | Display | PDB format |
PDBx/mmJSON format | 5jjr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jj/5jjr ftp://data.pdbj.org/pub/pdb/validation_reports/jj/5jjr | HTTPS FTP |
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-Related structure data
Related structure data | 5i3pC 5i3qC 5jjsC 5k5mC 4v0qS C: citing same article (ref.) 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 102830.633 Da / Num. of mol.: 1 / Fragment: UNP residues 2494-3385 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dengue virus 3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6DLV0, UniProt: Q6YMS4*PLUS |
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-Non-polymers , 7 types, 489 molecules
#2: Chemical | #3: Chemical | ChemComp-SAH / | #4: Chemical | ChemComp-68E / | #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-MG / | #7: Chemical | #8: 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: 2.39 Å3/Da / Density % sol: 48.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M Magnesium Formate 1mM TCEP 18% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 12, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→50 Å / Num. obs: 67993 / % possible obs: 99 % / Redundancy: 6.5 % / Biso Wilson estimate: 19.33 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 10.04 |
Reflection shell | Resolution: 1.99→2.11 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4V0Q Resolution: 1.99→47.3 Å / Cor.coef. Fo:Fc: 0.9174 / Cor.coef. Fo:Fc free: 0.8828 / SU R Cruickshank DPI: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.162 / SU Rfree Blow DPI: 0.15 / SU Rfree Cruickshank DPI: 0.148
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Displacement parameters | Biso mean: 23.75 Å2
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Refine analyze | Luzzati coordinate error obs: 0.212 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.99→47.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.99→2.04 Å / Total num. of bins used: 20
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