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Yorodumi- PDB-3kq7: Structure of human p38alpha with N-[4-methyl-3-(6-{[2-(1-methylpy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kq7 | ||||||
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Title | Structure of human p38alpha with N-[4-methyl-3-(6-{[2-(1-methylpyrrolidin-2-yl)ethyl]amino}pyridine-3-amido)phenyl]-2-(morpholin-4-yl)pyridine-4-carboxamide | ||||||
Components | Mitogen-activated protein kinase p38 alpha | ||||||
Keywords | TRANSFERASE / P38ALPHA KINASE / ALTERNATIVE SPLICING / ATP BINDING / CYTOPLASM / KINASE / NUCLEOTIDE-BINDING / NUCLEUS / PHOSPHOPROTEIN / POLYMORPHISM / SERINE/THREONINE-PROTEIN KINASE | ||||||
Function / homology | Function and homology information positive regulation of cyclase activity / stress-activated protein kinase signaling cascade / 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 cyclase activity / stress-activated protein kinase signaling cascade / 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 / DSCAM interactions / 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 / 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 / regulation of cytokine production involved in inflammatory response / ERK/MAPK targets / 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 / MAP kinase activity / regulation of ossification / cellular response to vascular endothelial growth factor stimulus / mitogen-activated protein kinase / signal transduction in response to DNA damage / positive regulation of myoblast differentiation / 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 / response to muscle stretch / positive regulation of interleukin-12 production / positive regulation of brown fat cell differentiation / osteoclast differentiation / positive regulation of erythrocyte differentiation / DNA damage checkpoint signaling / activated TAK1 mediates p38 MAPK activation / cellular response to ionizing radiation / stem cell differentiation / positive regulation of glucose import / NOD1/2 Signaling Pathway / response to insulin / bone development / negative regulation of canonical Wnt signaling pathway / placenta development / 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 / 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Cheng, R.K.Y. / Barker, J. / Whittaker, M. | ||||||
Citation | Journal: TO BE PUBLISHED Title: Structure of human p38alpha with N-[4-methyl-3-(6-{[2-(1-methylpyrrolidin-2-yl)ethyl]amino}pyridine-3-amido)phenyl]-2-(morpholin-4-yl)pyridine-4-carboxamide Authors: Cheng, R.K.Y. / Barker, J. / Whittaker, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kq7.cif.gz | 96.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kq7.ent.gz | 71.4 KB | Display | PDB format |
PDBx/mmJSON format | 3kq7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kq7_validation.pdf.gz | 717.4 KB | Display | wwPDB validaton report |
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Full document | 3kq7_full_validation.pdf.gz | 726.6 KB | Display | |
Data in XML | 3kq7_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | 3kq7_validation.cif.gz | 31 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kq/3kq7 ftp://data.pdbj.org/pub/pdb/validation_reports/kq/3kq7 | 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: 43514.543 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: pET15b / Production host: Escherichia coli (E. coli) References: UniProt: Q16539, mitogen-activated protein kinase | ||
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#2: Chemical | ChemComp-KQ7 / | ||
#3: Chemical | ChemComp-ACT / #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: 2.76 Å3/Da / Density % sol: 55.48 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 14-16%(w/v) PEG8000, 300mM Magnesium acetate, 100mM Hepes pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 31, 2004 / Details: VARIMAX MIRRORS |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→62.76 Å / Num. obs: 45051 / % possible obs: 98.9 % / Observed criterion σ(I): 1.9 / Redundancy: 3.26 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 1.81 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 2.3 / Num. unique all: 4463 / % possible all: 92.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1WFC Resolution: 1.8→16.72 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.437 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.941 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→16.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.797→1.843 Å / Total num. of bins used: 20
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