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Yorodumi- PDB-3c5u: P38 ALPHA map kinase complexed with a benzothiazole based inhibitor -
+Open data
-Basic information
Entry | Database: PDB / ID: 3c5u | ||||||
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Title | P38 ALPHA map kinase complexed with a benzothiazole based inhibitor | ||||||
Components | Mitogen-activated protein kinase 14MAPK14 | ||||||
Keywords | TRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / KINASE / P38 MAP KINASE / Alternative splicing / ATP-binding / Cytoplasm / Nucleotide-binding / Nucleus / Phosphoprotein | ||||||
Function / homology | Function and homology information positive regulation of cyclase activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / CD163 mediating an anti-inflammatory response / regulation of synaptic membrane adhesion / stress-induced premature senescence / cell surface receptor protein serine/threonine kinase signaling pathway / 3'-UTR-mediated mRNA stabilization / KSRP (KHSRP) binds and destabilizes mRNA / DSCAM interactions / cartilage condensation ...positive regulation of cyclase activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / CD163 mediating an anti-inflammatory response / regulation of synaptic membrane adhesion / stress-induced premature senescence / cell surface receptor protein serine/threonine kinase signaling pathway / 3'-UTR-mediated mRNA stabilization / KSRP (KHSRP) binds and destabilizes mRNA / DSCAM interactions / cartilage condensation / cellular response to UV-B / Platelet sensitization by LDL / stress-activated protein kinase signaling cascade / mitogen-activated protein kinase p38 binding / positive regulation of myoblast fusion / positive regulation of muscle cell differentiation / negative regulation of hippo signaling / positive regulation of myotube differentiation / NFAT protein binding / Myogenesis / glucose import / Activation of the AP-1 family of transcription factors / ERK/MAPK targets / regulation of cytokine production involved in inflammatory response / p38MAPK cascade / fatty acid oxidation / cellular response to lipoteichoic acid / MAP kinase kinase activity / response to dietary excess / response to muramyl dipeptide / RHO GTPases Activate NADPH Oxidases / regulation of ossification / MAP kinase activity / mitogen-activated protein kinase / cellular response to vascular endothelial growth factor stimulus / positive regulation of myoblast differentiation / chondrocyte differentiation / vascular endothelial growth factor receptor signaling pathway / stress-activated MAPK cascade / signal transduction in response to DNA damage / skeletal muscle tissue development / lipopolysaccharide-mediated signaling pathway / positive regulation of cardiac muscle cell proliferation / negative regulation of inflammatory response to antigenic stimulus / p38MAPK events / striated muscle cell differentiation / response to muscle stretch / positive regulation of brown fat cell differentiation / positive regulation of interleukin-12 production / osteoclast differentiation / positive regulation of erythrocyte differentiation / placenta development / DNA damage checkpoint signaling / activated TAK1 mediates p38 MAPK activation / cellular response to ionizing radiation / stem cell differentiation / positive regulation of glucose import / response to insulin / NOD1/2 Signaling Pathway / bone development / cell morphogenesis / negative regulation of canonical Wnt signaling pathway / platelet activation / cellular response to virus / osteoblast differentiation / VEGFA-VEGFR2 Pathway / spindle pole / positive regulation of protein import into nucleus / ADP signalling through P2Y purinoceptor 1 / glucose metabolic process / positive regulation of reactive oxygen species metabolic process / chemotaxis / cellular senescence / cellular response to tumor necrosis factor / peptidyl-serine phosphorylation / protein phosphatase binding / angiogenesis / secretory granule lumen / Oxidative Stress Induced Senescence / cellular response to lipopolysaccharide / Regulation of TP53 Activity through Phosphorylation / ficolin-1-rich granule lumen / transcription by RNA polymerase II / cell surface receptor signaling pathway / intracellular signal transduction / nuclear speck / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / apoptotic process / Neutrophil degranulation / positive regulation of gene expression / regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular region / nucleoplasm / ATP binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Sack, J.S. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2008 Title: Benzothiazole based inhibitors of p38alpha MAP kinase. Authors: Liu, C. / Lin, J. / Pitt, S. / Zhang, R.F. / Sack, J.S. / Kiefer, S.E. / Kish, K. / Doweyko, A.M. / Zhang, H. / Marathe, P.H. / Trzaskos, J. / Mckinnon, M. / Dodd, J.H. / Barrish, J.C. / ...Authors: Liu, C. / Lin, J. / Pitt, S. / Zhang, R.F. / Sack, J.S. / Kiefer, S.E. / Kish, K. / Doweyko, A.M. / Zhang, H. / Marathe, P.H. / Trzaskos, J. / Mckinnon, M. / Dodd, J.H. / Barrish, J.C. / Schieven, G.L. / Leftheris, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3c5u.cif.gz | 84.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c5u.ent.gz | 64 KB | Display | PDB format |
PDBx/mmJSON format | 3c5u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/3c5u ftp://data.pdbj.org/pub/pdb/validation_reports/c5/3c5u | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 42105.004 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK14, CSBP, CSBP1, CSBP2, CSPB1, MXI2 / Cell line (production host): BL21 DE3 / Production host: Escherichia coli (E. coli) References: UniProt: Q16539, mitogen-activated protein kinase | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.32 Å3/Da / Density % sol: 71.55 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 29, 2004 / Details: MICROMAX CONFOCAL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 17473 / % possible obs: 91.7 % / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 76.615 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 1.5 / % possible all: 51.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→18.26 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 71.64 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→18.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.97 Å / Total num. of bins used: 9
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