+Open data
-Basic information
Entry | Database: PDB / ID: 7bdq | ||||||
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Title | MAPK14 bound with SR300 | ||||||
Components | Mitogen-activated protein kinase 14 | ||||||
Keywords | TRANSFERASE / p38a / Inhibitor / MAPK14 / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information 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 ...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 / positive regulation of myoblast fusion / cellular response to UV-B / mitogen-activated protein kinase p38 binding / positive regulation of myotube differentiation / NFAT protein binding / glucose import / negative regulation of hippo signaling / regulation of cytokine production involved in inflammatory response / p38MAPK cascade / fatty acid oxidation / cellular response to lipoteichoic acid / response to muramyl dipeptide / response to dietary excess / MAP kinase activity / regulation of ossification / cellular response to vascular endothelial growth factor stimulus / mitogen-activated protein kinase / 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 / 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 / placenta development / positive regulation of glucose import / stem cell differentiation / cellular response to ionizing radiation / response to insulin / bone development / negative regulation of canonical Wnt signaling pathway / 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 / cellular response to tumor necrosis factor / kinase activity / peptidyl-serine phosphorylation / protein phosphatase binding / cellular response to lipopolysaccharide / 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 / DNA damage response / glutamatergic synapse / regulation of transcription by RNA polymerase II / positive regulation of gene expression / regulation of DNA-templated transcription / apoptotic process / 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: 2.75 Å | ||||||
Authors | Schroeder, M. / Roehm, S. / Joerger, A. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: J.Med.Chem. / Year: 2021 Title: Development of a Selective Dual Discoidin Domain Receptor (DDR)/p38 Kinase Chemical Probe. Authors: Rohm, S. / Berger, B.T. / Schroder, M. / Chatterjee, D. / Mathea, S. / Joerger, A.C. / Pinkas, D.M. / Bufton, J.C. / Tjaden, A. / Kovooru, L. / Kudolo, M. / Pohl, C. / Bullock, A.N. / ...Authors: Rohm, S. / Berger, B.T. / Schroder, M. / Chatterjee, D. / Mathea, S. / Joerger, A.C. / Pinkas, D.M. / Bufton, J.C. / Tjaden, A. / Kovooru, L. / Kudolo, M. / Pohl, C. / Bullock, A.N. / Muller, S. / Laufer, S. / Knapp, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bdq.cif.gz | 149.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bdq.ent.gz | 115.9 KB | Display | PDB format |
PDBx/mmJSON format | 7bdq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bdq_validation.pdf.gz | 729.6 KB | Display | wwPDB validaton report |
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Full document | 7bdq_full_validation.pdf.gz | 731.8 KB | Display | |
Data in XML | 7bdq_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 7bdq_validation.cif.gz | 13.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bd/7bdq ftp://data.pdbj.org/pub/pdb/validation_reports/bd/7bdq | HTTPS FTP |
-Related structure data
Related structure data | 7bcmC 7bdoC 7be4C 7be5C 7be6C 5larS S: Starting model for refinement C: citing same article (ref.) |
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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: 41395.211 Da / Num. of mol.: 1 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, mitogen-activated protein kinase | ||||||
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#2: Chemical | ChemComp-TJZ / ~{ | ||||||
#3: Chemical | #4: Chemical | ChemComp-MES / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.32 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 14% HMW PgSmear, 0.1M MES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 1, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.75→48.95 Å / Num. obs: 9622 / % possible obs: 99.6 % / Redundancy: 4.4 % / CC1/2: 0.977 / Rmerge(I) obs: 0.217 / Rpim(I) all: 0.11 / Rrim(I) all: 0.244 / Net I/σ(I): 5.9 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5lar Resolution: 2.75→48.9 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.886 / SU B: 36.044 / SU ML: 0.35 / SU R Cruickshank DPI: 0.3594 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.398 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 110 Å2 / Biso mean: 47.177 Å2 / Biso min: 19.42 Å2
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Refinement step | Cycle: final / Resolution: 2.75→48.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.822 Å / Rfactor Rfree error: 0 / 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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