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Yorodumi- PDB-3fyj: Crystal structure of an optimzied benzothiophene inhibitor bound ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fyj | ||||||
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Title | Crystal structure of an optimzied benzothiophene inhibitor bound to MAPKAP Kinase-2 (MK-2) | ||||||
Components | MAP kinase-activated protein kinase 2 | ||||||
Keywords | TRANSFERASE / MK-2 / MK2 / MAPKAP-2 / Ser/Thr kinase / MAP kinase / Alternative splicing / ATP-binding / Kinase / Nucleotide-binding / Phosphoprotein / Polymorphism / Serine/threonine-protein kinase | ||||||
Function / homology | Function and homology information macropinocytosis / CREB phosphorylation / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / leukotriene metabolic process / Synthesis of Leukotrienes (LT) and Eoxins (EX) / calcium-dependent protein serine/threonine kinase activity / regulation of tumor necrosis factor production / regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of macrophage cytokine production ...macropinocytosis / CREB phosphorylation / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / leukotriene metabolic process / Synthesis of Leukotrienes (LT) and Eoxins (EX) / calcium-dependent protein serine/threonine kinase activity / regulation of tumor necrosis factor production / regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of macrophage cytokine production / mitogen-activated protein kinase binding / regulation of interleukin-6 production / calcium/calmodulin-dependent protein kinase activity / 3'-UTR-mediated mRNA stabilization / toll-like receptor signaling pathway / p38MAPK cascade / inner ear development / Regulation of HSF1-mediated heat shock response / cellular response to vascular endothelial growth factor stimulus / vascular endothelial growth factor receptor signaling pathway / regulation of cellular response to heat / p38MAPK events / regulation of mRNA stability / response to cytokine / activated TAK1 mediates p38 MAPK activation / Regulation of TNFR1 signaling / VEGFA-VEGFR2 Pathway / positive regulation of tumor necrosis factor production / MAPK cascade / peptidyl-serine phosphorylation / Oxidative Stress Induced Senescence / response to lipopolysaccharide / non-specific serine/threonine protein kinase / calmodulin binding / protein kinase activity / intracellular signal transduction / inflammatory response / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / DNA damage response / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å | ||||||
Authors | Kurumbail, R.G. / Caspers, N. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2009 Title: Benzothiophene inhibitors of MK2. Part 2: improvements in kinase selectivity and cell potency. Authors: Anderson, D.R. / Meyers, M.J. / Kurumbail, R.G. / Caspers, N. / Poda, G.I. / Long, S.A. / Pierce, B.S. / Mahoney, M.W. / Mourey, R.J. / Parikh, M.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fyj.cif.gz | 66.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fyj.ent.gz | 48.5 KB | Display | PDB format |
PDBx/mmJSON format | 3fyj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fyj_validation.pdf.gz | 635.1 KB | Display | wwPDB validaton report |
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Full document | 3fyj_full_validation.pdf.gz | 665.6 KB | Display | |
Data in XML | 3fyj_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 3fyj_validation.cif.gz | 20.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/3fyj ftp://data.pdbj.org/pub/pdb/validation_reports/fy/3fyj | HTTPS FTP |
-Related structure data
Related structure data | 3fykC 3fz1C 2p3gS 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: 37897.750 Da / Num. of mol.: 1 / Fragment: MK-2 kinase module and the auto-inhibitory domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAPKAP-2, MAPKAPK2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 References: UniProt: P49137, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-B97 / ( |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.59 Å3/Da / Density % sol: 73.19 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: MK-2 protein at 5 mg/ml is equilibrated against a well solution of 1.6 - 2.0 M Sodium malonate at pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC / Detector: CCD / Date: Mar 13, 2005 | ||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.7→29.51 Å / Num. obs: 6885 / % possible obs: 85.6 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 18.664 | ||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2P3G Resolution: 3.8→29.51 Å / Cor.coef. Fo:Fc: 0.848 / Cor.coef. Fo:Fc free: 0.79 / Occupancy max: 1 / Occupancy min: 1 / SU B: 66.192 / SU ML: 0.876 / Cross valid method: THROUGHOUT / ESU R Free: 0.977 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 80 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.8→29.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.801→3.899 Å / Total num. of bins used: 20
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