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Yorodumi- PDB-4kiq: Crystal structure of mitogen-activated protein kinase 14 (P38-H5)... -
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-Basic information
Entry | Database: PDB / ID: 4kiq | ||||||
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Title | Crystal structure of mitogen-activated protein kinase 14 (P38-H5) complex with ETHYL 6-((5-(CYCLOPROPYLCARBAMOYL)-2-METHYLPHENYL)CARBAMOYL)-1H-INDOLE-1-CARBOXYLATE | ||||||
Components | Mitogen-activated protein kinase 14 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / SERINE/THREONINE-PROTEIN KINASE / KINASE / TRANSFERASE / P38 MAP KINASE / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information stress-activated protein kinase signaling cascade / 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 / cartilage condensation ...stress-activated protein kinase signaling cascade / 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 / cartilage condensation / positive regulation of myoblast fusion / cellular response to UV-B / Platelet sensitization by LDL / mitogen-activated protein kinase p38 binding / positive regulation of muscle cell differentiation / positive regulation of myotube differentiation / NFAT protein binding / Myogenesis / D-glucose import / regulation of cytokine production involved in inflammatory response / Activation of the AP-1 family of transcription factors / ERK/MAPK targets / p38MAPK cascade / Regulation of MITF-M-dependent genes involved in pigmentation / 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 / MAP kinase activity / regulation of ossification / positive regulation of myoblast differentiation / cellular response to vascular endothelial growth factor stimulus / mitogen-activated protein kinase / negative regulation of hippo signaling / signal transduction in response to DNA damage / chondrocyte differentiation / vascular endothelial growth factor receptor signaling pathway / stress-activated MAPK cascade / skeletal muscle tissue development / positive regulation of cardiac muscle cell proliferation / lipopolysaccharide-mediated signaling pathway / negative regulation of inflammatory response to antigenic stimulus / p38MAPK events / striated muscle cell differentiation / positive regulation of interleukin-12 production / response to muscle stretch / positive regulation of brown fat cell differentiation / bone development / osteoclast differentiation / positive regulation of erythrocyte differentiation / DNA damage checkpoint signaling / stem cell differentiation / activated TAK1 mediates p38 MAPK activation / positive regulation of D-glucose import / cellular response to ionizing radiation / response to insulin / NOD1/2 Signaling Pathway / placenta development / negative regulation of canonical Wnt signaling pathway / cell morphogenesis / cellular response to virus / platelet activation / VEGFA-VEGFR2 Pathway / spindle pole / positive regulation of protein import into nucleus / osteoblast differentiation / ADP signalling through P2Y purinoceptor 1 / glucose metabolic process / chemotaxis / positive regulation of reactive oxygen species metabolic process / cellular senescence / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / peptidyl-serine phosphorylation / protein phosphatase binding / angiogenesis / secretory granule lumen / Oxidative Stress Induced Senescence / 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 / Neutrophil degranulation / positive regulation of gene expression / regulation of transcription by RNA polymerase II / apoptotic process / 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: 2.5 Å | ||||||
Authors | Sack, J.S. / Tokarski, J.S. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2013 Title: The Identification of Novel P38-Alpha Isoform Selective Kinase Inhibitors Having an Unprecedented P38-Alpha Binding Mode Authors: Wrobleski, S.T. / Lin, S. / Murali Dhar, T.G. / Dyckman, A.J. / Li, T. / Pitt, S. / Zhang, R. / Fan, Y. / Doweyko, A.M. / Tokarski, J.S. / Kish, K.F. / Kiefer, S.E. / Sack, J.S. / Newitt, J. ...Authors: Wrobleski, S.T. / Lin, S. / Murali Dhar, T.G. / Dyckman, A.J. / Li, T. / Pitt, S. / Zhang, R. / Fan, Y. / Doweyko, A.M. / Tokarski, J.S. / Kish, K.F. / Kiefer, S.E. / Sack, J.S. / Newitt, J.A. / Witmer, M.R. / McKinnon, M. / Barrish, J.C. / Dodd, J.H. / 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 | 4kiq.cif.gz | 288.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kiq.ent.gz | 233.7 KB | Display | PDB format |
PDBx/mmJSON format | 4kiq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4kiq_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 4kiq_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 4kiq_validation.xml.gz | 51 KB | Display | |
Data in CIF | 4kiq_validation.cif.gz | 72.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ki/4kiq ftp://data.pdbj.org/pub/pdb/validation_reports/ki/4kiq | HTTPS FTP |
-Related structure data
Related structure data | 4kinC 4kipC 3s4qS 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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Unit cell |
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-Components
#1: Protein | Mass: 42105.004 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CSBP, CSBP1, CSBP2, CSPB1, MAPK14, MXI2, SAPK2A / Cell line (production host): BL21 DE3 / Production host: Escherichia coli (E. coli) References: UniProt: Q16539, mitogen-activated protein kinase #2: Chemical | ChemComp-1RA / #3: Water | ChemComp-HOH / | |
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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: 2.2 Å3/Da / Density % sol: 44.16 % |
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Crystal grow | pH: 6 Details: 1-6% (W/V) PEG-4K 50 MM MES, PH 6.0, 5MM MAGNESIUM SULFATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 14, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 49302 / % possible obs: 96.5 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 48.24 Å2 / Rmerge(I) obs: 0.022 / Net I/σ(I): 39.2 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.058 / Mean I/σ(I) obs: 15.6 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3S4Q Resolution: 2.5→42.88 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.8964 / SU R Cruickshank DPI: 0.874 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 39.52 Å2
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Refine analyze | Luzzati coordinate error obs: 0.281 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→42.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.56 Å / Total num. of bins used: 20
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