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Yorodumi- PDB-5ekx: DENGUE 3 NS5 METHYLTRANSFERASE BOUND TO S-ADENOSYLMETHIONINE AND ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ekx | ||||||
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Title | DENGUE 3 NS5 METHYLTRANSFERASE BOUND TO S-ADENOSYLMETHIONINE AND FRAGMENT NB2E11 | ||||||
Components | NS5 METHYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / NS5 methyltransferase dengue virus / fragment-based drug design | ||||||
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 / double-stranded RNA binding / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity ...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 / double-stranded RNA binding / nucleoside-triphosphate phosphatase / 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 perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / serine-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 / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Dengue virus type 3 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å | ||||||
Authors | Barral, K. / Bricogne, G. / Sharff, A. | ||||||
Funding support | France, 1items
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Citation | Journal: Eur.J.Med.Chem. / Year: 2016 Title: Discovery of novel dengue virus NS5 methyltransferase non-nucleoside inhibitors by fragment-based drug design. Authors: Benmansour, F. / Trist, I. / Coutard, B. / Decroly, E. / Querat, G. / Brancale, A. / Barral, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ekx.cif.gz | 230.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ekx.ent.gz | 184.2 KB | Display | PDB format |
PDBx/mmJSON format | 5ekx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ekx_validation.pdf.gz | 943.4 KB | Display | wwPDB validaton report |
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Full document | 5ekx_full_validation.pdf.gz | 945.8 KB | Display | |
Data in XML | 5ekx_validation.xml.gz | 24 KB | Display | |
Data in CIF | 5ekx_validation.cif.gz | 34.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/5ekx ftp://data.pdbj.org/pub/pdb/validation_reports/ek/5ekx | HTTPS FTP |
-Related structure data
Related structure data | 5e9qC 5ec8C 5ehgC 5ehiC 5eifC 5eiwC 3p97S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31206.812 Da / Num. of mol.: 2 / Fragment: residues 2491-2766 Source method: isolated from a genetically manipulated source Details: synthetic gene Source: (gene. exp.) Dengue virus type 3 (strain Philippines/H87/1956) Strain: Philippines/H87/1956 / Plasmid: PMCOX20A / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): rosetta References: UniProt: P27915, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase, mRNA (guanine-N7)-methyltransferase, methyltransferase cap1, RNA-directed RNA polymerase #2: Chemical | #3: Chemical | ChemComp-2CQ / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 25% PEG 8000 100mM Tris 200mM NaCl 20mM Trisodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.99187 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 21, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99187 Å / Relative weight: 1 |
Reflection | Resolution: 1.757→61.235 Å / Num. obs: 54703 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 28.99 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.76→1.81 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.598 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3P97 Resolution: 1.76→51.49 Å / Cor.coef. Fo:Fc: 0.9326 / Cor.coef. Fo:Fc free: 0.9139 / SU R Cruickshank DPI: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.121 / SU Rfree Blow DPI: 0.114 / SU Rfree Cruickshank DPI: 0.111
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Displacement parameters | Biso mean: 39.92 Å2
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Refine analyze | Luzzati coordinate error obs: 0.262 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.76→51.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.76→1.81 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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