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Yorodumi- PDB-6t8x: Crystal structure of MAPKAPK2 (MK2) complexed with PF-3644022 and... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6t8x | ||||||
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Title | Crystal structure of MAPKAPK2 (MK2) complexed with PF-3644022 and 5-(4-bromophenyl)-N-[4-(1-piperazinyl)phenyl]-N-(2-pyridinylmethyl)-2-furancarboxamide | ||||||
Components | MAP kinase-activated protein kinase 2 | ||||||
Keywords | IMMUNE SYSTEM / kinase / non-ATP competitive inhibitor / type4 | ||||||
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: 2.81 Å | ||||||
Authors | Beaumont, E.J. / Barker, J. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of MAPKAPK2 (MK2) complexed with PF-3644022 and 5-(4-bromophenyl)-N-[4-(1-piperazinyl)phenyl]-N-(2-pyridinylmethyl)-2-furancarboxamide Authors: Beaumont, E.J. / Barker, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6t8x.cif.gz | 350.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6t8x.ent.gz | 286.2 KB | Display | PDB format |
PDBx/mmJSON format | 6t8x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6t8x_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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Full document | 6t8x_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 6t8x_validation.xml.gz | 58.4 KB | Display | |
Data in CIF | 6t8x_validation.cif.gz | 76.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t8/6t8x ftp://data.pdbj.org/pub/pdb/validation_reports/t8/6t8x | 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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Unit cell |
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-Components
#1: Protein | Mass: 36812.258 Da / Num. of mol.: 6 / Mutation: T222E, T334E Source method: isolated from a genetically manipulated source Details: B97 and 5-(4-bromophenyl)-N-[4-(1-piperazinyl)phenyl]-N-(2-pyridinylmethyl)-2-furancarboxamide Source: (gene. exp.) Homo sapiens (human) / Gene: MAPKAPK2 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P49137, non-specific serine/threonine protein kinase #2: Chemical | ChemComp-B97 / ( #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-MW8 / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 3.39 Å3/Da / Density % sol: 63.74 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 1.3M NaMalonate, 0.1M Hepes pH6.0, 0.5% jeffamine ED2003 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.81→143.67 Å / Num. obs: 68678 / % possible obs: 100 % / Redundancy: 6.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.1 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.81→2.88 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1.495 / Mean I/σ(I) obs: 1 / Num. unique obs: 28351 / CC1/2: 0.668 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NY3 Resolution: 2.81→120 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.907 / SU R Cruickshank DPI: 0.66 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.603 / SU Rfree Blow DPI: 0.302 / SU Rfree Cruickshank DPI: 0.312
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Displacement parameters | Biso max: 146.62 Å2 / Biso mean: 92.85 Å2 / Biso min: 59.68 Å2
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Refine analyze | Luzzati coordinate error obs: 0.45 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.81→120 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.81→3 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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