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Yorodumi- PDB-5hmz: Dengue serotype 3 RNA-dependent RNA polymerase bound to compound 23 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hmz | ||||||
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Title | Dengue serotype 3 RNA-dependent RNA polymerase bound to compound 23 | ||||||
Components | RNA-directed RNA polymerase NS5 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Inhibitor Complex Polymerase / TRANSFERASE-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 / structural molecule activity / virion attachment to host cell / virion membrane / 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 | Noble, C.G. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2016 Title: Discovery of Potent Non-Nucleoside Inhibitors of Dengue Viral RNA-Dependent RNA Polymerase from a Fragment Hit Using Structure-Based Drug Design Authors: Yokokawa, F. / Nilar, S. / Noble, C.G. / Lim, S.P. / Rao, R. / Tania, S. / Wang, G. / Lee, G. / Hunziker, J. / Karuna, R. / Manjunatha, U. / Shi, P.Y. / Smith, P.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hmz.cif.gz | 149.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hmz.ent.gz | 112.3 KB | Display | PDB format |
PDBx/mmJSON format | 5hmz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hm/5hmz ftp://data.pdbj.org/pub/pdb/validation_reports/hm/5hmz | HTTPS FTP |
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-Related structure data
Related structure data | 5hmwC 5hmxC 5hmyC 5hn0C 4hhjS 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
#1: Protein | Mass: 73624.867 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 2762-3390 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, RNA-directed RNA polymerase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-LNZ / | #4: Water | ChemComp-HOH / | Sequence details | residue 374 GLU is a naturally occurred mutation in the viral sequence. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.66 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M TRIS, 25% PEG 550 MME |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å | ||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 28, 2013 | ||||||||||||||||||
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→118.59 Å / Num. obs: 56377 / % possible obs: 99.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 35.39 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Net I/σ(I): 19.7 | ||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HHJ Resolution: 1.99→39.8 Å / Cor.coef. Fo:Fc: 0.9406 / Cor.coef. Fo:Fc free: 0.9263 / SU R Cruickshank DPI: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.148 / SU Rfree Blow DPI: 0.132 / SU Rfree Cruickshank DPI: 0.129
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Displacement parameters | Biso max: 135.86 Å2 / Biso mean: 42.36 Å2 / Biso min: 18.08 Å2
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Refine analyze | Luzzati coordinate error obs: 0.215 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.99→39.8 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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