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Yorodumi- PDB-3fpm: Crystal Structure of a Squarate Inhibitor bound to MAPKAP Kinase-2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fpm | ||||||
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Title | Crystal Structure of a Squarate Inhibitor bound to MAPKAP Kinase-2 | ||||||
Components | MAP kinase-activated protein kinase 2 | ||||||
Keywords | TRANSFERASE / ATP-binding / Alternative splicing / 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 / mitogen-activated protein kinase binding ...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 / mitogen-activated protein kinase binding / positive regulation of macrophage cytokine production / 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 / MAPK cascade / positive regulation of tumor necrosis factor production / peptidyl-serine phosphorylation / Oxidative Stress Induced Senescence / response to lipopolysaccharide / calmodulin binding / non-specific serine/threonine protein kinase / 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: 3.3 Å | ||||||
Authors | Parris, K.D. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2009 Title: Identification and SAR of squarate inhibitors of mitogen activated protein kinase-activated protein kinase 2 (MK-2) Authors: Lovering, F. / Kirincich, S. / Wang, W. / Combs, K. / Resnick, L. / Sabalski, J.E. / Butera, J. / Liu, J. / Parris, K. / Telliez, J.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fpm.cif.gz | 71.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fpm.ent.gz | 54.1 KB | Display | PDB format |
PDBx/mmJSON format | 3fpm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fpm_validation.pdf.gz | 685.5 KB | Display | wwPDB validaton report |
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Full document | 3fpm_full_validation.pdf.gz | 688 KB | Display | |
Data in XML | 3fpm_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 3fpm_validation.cif.gz | 15.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fp/3fpm ftp://data.pdbj.org/pub/pdb/validation_reports/fp/3fpm | HTTPS FTP |
-Related structure data
Related structure data | 1ny3S 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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Details | The asymmetric unit of a crystal structure contains the biological unit |
-Components
#1: Protein | Mass: 37652.527 Da / Num. of mol.: 1 / Fragment: Protein kinase domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAPKAPK2 / Plasmid: pET16b / 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-793 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.57 Å3/Da / Density % sol: 73.08 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 1600 mM Sodium Malonate pH 5, 1 % MPD, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 24, 2003 |
Radiation | Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→30 Å / Num. obs: 10421 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1NY3 Resolution: 3.3→30 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.872 / SU B: 25.48 / SU ML: 0.421 / Cross valid method: THROUGHOUT / ESU R: 0.756 / ESU R Free: 0.531 / 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: 127.583 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.388 Å / Total num. of bins used: 20
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