+Open data
-Basic information
Entry | Database: PDB / ID: 1yw2 | ||||||
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Title | Mutated Mus Musculus P38 Kinase (mP38) | ||||||
Components | Mitogen-activated protein kinase 14 | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information DSCAM interactions / p38MAPK events / Activation of the AP-1 family of transcription factors / Platelet sensitization by LDL / RHO GTPases Activate NADPH Oxidases / ERK/MAPK targets / activated TAK1 mediates p38 MAPK activation / NOD1/2 Signaling Pathway / ADP signalling through P2Y purinoceptor 1 / Oxidative Stress Induced Senescence ...DSCAM interactions / p38MAPK events / Activation of the AP-1 family of transcription factors / Platelet sensitization by LDL / RHO GTPases Activate NADPH Oxidases / ERK/MAPK targets / activated TAK1 mediates p38 MAPK activation / NOD1/2 Signaling Pathway / ADP signalling through P2Y purinoceptor 1 / Oxidative Stress Induced Senescence / Regulation of TP53 Activity through Phosphorylation / Myogenesis / VEGFA-VEGFR2 Pathway / regulation of synaptic membrane adhesion / stress-induced premature senescence / cell surface receptor protein serine/threonine kinase signaling pathway / cartilage condensation / cellular response to UV-B / mitogen-activated protein kinase p38 binding / positive regulation of myoblast fusion / negative regulation of hippo signaling / positive regulation of myotube differentiation / NFAT protein binding / glucose import / regulation of cytokine production involved in inflammatory response / p38MAPK cascade / fatty acid oxidation / cellular response to lipoteichoic acid / response to dietary excess / response to muramyl dipeptide / MAP kinase activity / regulation of ossification / 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 / skeletal muscle tissue development / lipopolysaccharide-mediated signaling pathway / positive regulation of cardiac muscle cell proliferation / striated muscle cell differentiation / response to muscle stretch / positive regulation of interleukin-12 production / positive regulation of brown fat cell differentiation / Neutrophil degranulation / osteoclast differentiation / positive regulation of erythrocyte differentiation / DNA damage checkpoint signaling / cellular response to ionizing radiation / stem cell differentiation / positive regulation of glucose import / response to insulin / bone development / negative regulation of canonical Wnt signaling pathway / placenta development / cell morphogenesis / cellular response to virus / spindle pole / positive regulation of protein import into nucleus / osteoblast differentiation / glucose metabolic process / positive regulation of reactive oxygen species metabolic process / MAPK cascade / kinase activity / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / peptidyl-serine phosphorylation / protein phosphatase binding / angiogenesis / transcription by RNA polymerase II / response to lipopolysaccharide / protein kinase activity / intracellular signal transduction / nuclear speck / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / apoptotic process / DNA damage response / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å | ||||||
Authors | Laughlin, S.K. / Clark, M.P. / Djung, J.F. / Golebiowski, A. / Brugel, T.A. / Sabat, M. / Bookland, R.G. / Laufersweiler, M.J. / Vanrens, J.C. / Townes, J.A. ...Laughlin, S.K. / Clark, M.P. / Djung, J.F. / Golebiowski, A. / Brugel, T.A. / Sabat, M. / Bookland, R.G. / Laufersweiler, M.J. / Vanrens, J.C. / Townes, J.A. / De, B. / Hsieh, L.C. / Xu, S.C. / Walter, R.L. / Mekel, M.J. / Janusz, M.J. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2005 Title: The development of new isoxazolone based inhibitors of tumor necrosis factor-alpha (TNF-alpha) production. Authors: Laughlin, S.K. / Clark, M.P. / Djung, J.F. / Golebiowski, A. / Brugel, T.A. / Sabat, M. / Bookland, R.G. / Laufersweiler, M.J. / Vanrens, J.C. / Townes, J.A. / De, B. / Hsieh, L.C. / Xu, S.C. ...Authors: Laughlin, S.K. / Clark, M.P. / Djung, J.F. / Golebiowski, A. / Brugel, T.A. / Sabat, M. / Bookland, R.G. / Laufersweiler, M.J. / Vanrens, J.C. / Townes, J.A. / De, B. / Hsieh, L.C. / Xu, S.C. / Walter, R.L. / Mekel, M.J. / Janusz, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yw2.cif.gz | 88.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yw2.ent.gz | 65.2 KB | Display | PDB format |
PDBx/mmJSON format | 1yw2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yw2_validation.pdf.gz | 749.3 KB | Display | wwPDB validaton report |
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Full document | 1yw2_full_validation.pdf.gz | 772.2 KB | Display | |
Data in XML | 1yw2_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 1yw2_validation.cif.gz | 27.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yw/1yw2 ftp://data.pdbj.org/pub/pdb/validation_reports/yw/1yw2 | HTTPS FTP |
-Related structure data
Related structure data | 1cm8S 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: 41292.137 Da / Num. of mol.: 1 / Mutation: S180A, Y182F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mapk14, Crk1, Csbp1, Csbp2 / Production host: Escherichia coli (E. coli) / References: UniProt: P47811, EC: 2.7.1.37 |
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#2: Chemical | ChemComp-PGJ / |
#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: 2.23 Å3/Da / Density % sol: 44.87 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 1500, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 19, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→50 Å / Num. all: 24876 / Num. obs: 24876 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Biso Wilson estimate: 40.58 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 19 |
Reflection shell | Resolution: 2.07→2.15 Å / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1CM8 Resolution: 2.01→50 Å
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Refinement step | Cycle: LAST / Resolution: 2.01→50 Å
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