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Yorodumi- PDB-5hn0: Dengue serotype 3 RNA-dependent RNA polymerase bound to compound 4 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hn0 | ||||||
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Title | Dengue serotype 3 RNA-dependent RNA polymerase bound to compound 4 | ||||||
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 / host cell mitochondrion / flavivirin / 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 / host cell mitochondrion / flavivirin / 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: 2.05 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 | 5hn0.cif.gz | 146.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hn0.ent.gz | 110.3 KB | Display | PDB format |
PDBx/mmJSON format | 5hn0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hn/5hn0 ftp://data.pdbj.org/pub/pdb/validation_reports/hn/5hn0 | HTTPS FTP |
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-Related structure data
Related structure data | 5hmwC 5hmxC 5hmyC 5hmzC 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-LNN / ( | #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: 2.81 Å3/Da / Density % sol: 56.28 % |
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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: X06DA / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 12, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.05→119.521 Å / Num. obs: 52621 / % possible obs: 100 % / Redundancy: 6.1 % / Biso Wilson estimate: 32.95 Å2 / Rsym value: 0.126 / Net I/av σ(I): 5.41 / Net I/σ(I): 9.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HHJ Resolution: 2.05→20.66 Å / Cor.coef. Fo:Fc: 0.9301 / Cor.coef. Fo:Fc free: 0.9005 / SU R Cruickshank DPI: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.156 / SU Rfree Blow DPI: 0.149 / SU Rfree Cruickshank DPI: 0.146
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Displacement parameters | Biso max: 152.18 Å2 / Biso mean: 43.28 Å2 / Biso min: 15.85 Å2
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Refine analyze | Luzzati coordinate error obs: 0.238 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.05→20.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.1 Å / Total num. of bins used: 20
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