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Yorodumi- PDB-6mo1: Structure of dengue virus protease with an allosteric Inhibitor t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6mo1 | ||||||
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Title | Structure of dengue virus protease with an allosteric Inhibitor that blocks replication | ||||||
Components | FLAVIVIRUS_NS2B/Peptidase S7 | ||||||
Keywords | VIRAL PROTEIN/INHIBITOR / Allosteric Inhibitor / Inhibitor / Complex / Protease / VIRAL PROTEIN / VIRAL PROTEIN-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 / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / 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 / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / membrane => GO:0016020 / RNA helicase activity / 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 / 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 / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Dengue virus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Lin, Y.-L. / Hua, Y. / Nie, S. / Wu, J. / Wu, F. / Huo, T. / Yao, Y. / Song, Y. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2019 Title: Discovery, X-ray Crystallography and Antiviral Activity of Allosteric Inhibitors of Flavivirus NS2B-NS3 Protease. Authors: Yao, Y. / Huo, T. / Lin, Y.L. / Nie, S. / Wu, F. / Hua, Y. / Wu, J. / Kneubehl, A.R. / Vogt, M.B. / Rico-Hesse, R. / Song, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mo1.cif.gz | 147.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mo1.ent.gz | 113.5 KB | Display | PDB format |
PDBx/mmJSON format | 6mo1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6mo1_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6mo1_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6mo1_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 6mo1_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mo/6mo1 ftp://data.pdbj.org/pub/pdb/validation_reports/mo/6mo1 | HTTPS FTP |
-Related structure data
Related structure data | 6mo0C 6mo2C 2fomS 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 26330.496 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dengue virus 2 / Production host: Escherichia coli (E. coli) / References: UniProt: B3RFT3, UniProt: Q91H74 #2: Chemical | |
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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: 2.5 Å3/Da / Density % sol: 50.82 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 35% PEG 200, 100 mM MES, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jun 25, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 14737 / % possible obs: 100 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.445 / Net I/σ(I): 11.48 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 7.8 % / Rmerge(I) obs: 2.409 / Mean I/σ(I) obs: 1.29 / Num. unique obs: 1464 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FOM Resolution: 3→47.38 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.839 / SU B: 51.727 / SU ML: 0.424 / Cross valid method: THROUGHOUT / ESU R Free: 0.475 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.881 Å2
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Refinement step | Cycle: 1 / Resolution: 3→47.38 Å
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Refine LS restraints |
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