+Open data
-Basic information
Entry | Database: PDB / ID: 3p8z | ||||||
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Title | Dengue Methyltransferase bound to a SAM-based inhibitor | ||||||
Components | Non-structural protein 5 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Methyltransferase / RNA / ER / 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 / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / 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 / double-stranded RNA binding / viral capsid / 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 / RNA-directed RNA polymerase / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / 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 3 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Noble, C.G. / Yap, L.J. / Lescar, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Small molecule inhibitors that selectively block dengue virus methyltransferase Authors: Lim, S.P. / Sonntag, L.S. / Noble, C. / Nilar, S.H. / Ng, R.H. / Zou, G. / Monaghan, P. / Chung, K.Y. / Dong, H. / Liu, B. / Bodenreider, C. / Lee, G. / Ding, M. / Chan, W.L. / Wang, G. / ...Authors: Lim, S.P. / Sonntag, L.S. / Noble, C. / Nilar, S.H. / Ng, R.H. / Zou, G. / Monaghan, P. / Chung, K.Y. / Dong, H. / Liu, B. / Bodenreider, C. / Lee, G. / Ding, M. / Chan, W.L. / Wang, G. / Jian, Y.L. / Chao, A.T. / Lescar, J. / Yin, Z. / Vedananda, T.R. / Keller, T.H. / Shi, P.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3p8z.cif.gz | 135.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3p8z.ent.gz | 103 KB | Display | PDB format |
PDBx/mmJSON format | 3p8z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3p8z_validation.pdf.gz | 933.3 KB | Display | wwPDB validaton report |
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Full document | 3p8z_full_validation.pdf.gz | 938.9 KB | Display | |
Data in XML | 3p8z_validation.xml.gz | 29.2 KB | Display | |
Data in CIF | 3p8z_validation.cif.gz | 45.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p8/3p8z ftp://data.pdbj.org/pub/pdb/validation_reports/p8/3p8z | HTTPS FTP |
-Related structure data
Related structure data | 3p97C 1l9kS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 30069.586 Da / Num. of mol.: 2 / Fragment: Methyltransferase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dengue virus 3 / Plasmid: GEX6P1 / Production host: Escherichia coli (E. coli) References: UniProt: C1KBQ3, UniProt: P27915*PLUS, mRNA (guanine-N7)-methyltransferase, methyltransferase cap1 #2: Chemical | ChemComp-36A / ( | #3: Chemical | ChemComp-SAH / | #4: 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: 2.43 Å3/Da / Density % sol: 49.39 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 8.5 / Details: pH 8.5, VAPOR DIFFUSION, temperature 291K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
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Detector | Date: Jun 15, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→51.78 Å / Num. obs: 64661 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1L9K Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.518 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.589 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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