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Yorodumi- PDB-3d83: Crystal structure of P38 kinase in complex with a biphenyl amide ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d83 | ||||||
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Title | Crystal structure of P38 kinase in complex with a biphenyl amide inhibitor | ||||||
Components | Mitogen-activated protein kinase 14 | ||||||
Keywords | TRANSFERASE / P38 / SERINE/THREONINE PROTEIN KINASE / MAP KINASE / ATP-binding / Nucleotide-binding / Nucleus / Phosphoprotein / Serine/threonine-protein kinase | ||||||
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 / Myogenesis / NFAT protein binding / 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 / cellular response to vascular endothelial growth factor stimulus / positive regulation of myoblast differentiation / negative regulation of hippo signaling / signal transduction in response to DNA damage / mitogen-activated protein kinase / chondrocyte differentiation / vascular endothelial growth factor receptor signaling pathway / positive regulation of cardiac muscle cell proliferation / lipopolysaccharide-mediated signaling pathway / stress-activated MAPK cascade / negative regulation of inflammatory response to antigenic stimulus / skeletal muscle tissue development / 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 / positive regulation of erythrocyte differentiation / osteoclast 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 / NOD1/2 Signaling Pathway / response to insulin / placenta development / negative regulation of canonical Wnt signaling pathway / cell morphogenesis / platelet activation / cellular response to virus / 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 / peptidyl-serine phosphorylation / cellular response to lipopolysaccharide / angiogenesis / protein phosphatase binding / 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 / FOURIER SYNTHESIS / Resolution: 1.9 Å | ||||||
Authors | Somers, D.O. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2008 Title: Biphenyl amide p38 kinase inhibitors 4: DFG-in and DFG-out binding modes. Authors: Angell, R.M. / Angell, T.D. / Bamborough, P. / Bamford, M.J. / Chung, C.W. / Cockerill, S.G. / Flack, S.S. / Jones, K.L. / Laine, D.I. / Longstaff, T. / Ludbrook, S. / Pearson, R. / Smith, K. ...Authors: Angell, R.M. / Angell, T.D. / Bamborough, P. / Bamford, M.J. / Chung, C.W. / Cockerill, S.G. / Flack, S.S. / Jones, K.L. / Laine, D.I. / Longstaff, T. / Ludbrook, S. / Pearson, R. / Smith, K.J. / Smee, P.A. / Somers, D.O. / Walker, A.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d83.cif.gz | 95.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d83.ent.gz | 71.2 KB | Display | PDB format |
PDBx/mmJSON format | 3d83.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3d83_validation.pdf.gz | 724.3 KB | Display | wwPDB validaton report |
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Full document | 3d83_full_validation.pdf.gz | 728 KB | Display | |
Data in XML | 3d83_validation.xml.gz | 19.6 KB | Display | |
Data in CIF | 3d83_validation.cif.gz | 30 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d8/3d83 ftp://data.pdbj.org/pub/pdb/validation_reports/d8/3d83 | HTTPS FTP |
-Related structure data
Related structure data | 1wfcS 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: 41375.195 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 / Plasmid: pRSETA / Production host: Escherichia coli (E. coli) / Strain (production host): BRL References: UniProt: Q16539, mitogen-activated protein kinase |
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#2: Chemical | ChemComp-GK6 / |
#3: Chemical | ChemComp-GOL / |
#4: 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: 3.07 Å3/Da / Density % sol: 59.97 % Description: THE BINARY COMPLEX HAS BEEN FORMED BY SOAKING AN APO-CRYSTAL |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.5 Details: Authors suggest to see publication for details, pH 6.5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 27, 2001 |
Radiation | Monochromator: Daresbury / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→35 Å / Num. obs: 34124 / % possible obs: 82.4 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.053 / Χ2: 0.992 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 1.7 / Num. unique all: 2939 / Χ2: 0.905 / % possible all: 72.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1WFC Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.596 / SU ML: 0.089 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.516 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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