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Yorodumi- PDB-7pvu: Crystal structure of p38alpha C162S in complex with CAS2094511-69... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pvu | |||||||||
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Title | Crystal structure of p38alpha C162S in complex with CAS2094511-69-8, P 1 21 1 | |||||||||
Components | Mitogen-activated protein kinase 14 | |||||||||
Keywords | ONCOPROTEIN / kinase / enzyme / inhibitor / ligand | |||||||||
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 / 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 / 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: 2.154 Å | |||||||||
Authors | Baginski, B. / Pous, J. / Gonzalez, L. / Macias, M.J. / Nebreda, A.R. | |||||||||
Funding support | Spain, 2items
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Citation | Journal: Nat Commun / Year: 2023 Title: Characterization of p38 alpha autophosphorylation inhibitors that target the non-canonical activation pathway. Authors: Gonzalez, L. / Diaz, L. / Pous, J. / Baginski, B. / Duran-Corbera, A. / Scarpa, M. / Brun-Heath, I. / Igea, A. / Martin-Malpartida, P. / Ruiz, L. / Pallara, C. / Esguerra, M. / Colizzi, F. / ...Authors: Gonzalez, L. / Diaz, L. / Pous, J. / Baginski, B. / Duran-Corbera, A. / Scarpa, M. / Brun-Heath, I. / Igea, A. / Martin-Malpartida, P. / Ruiz, L. / Pallara, C. / Esguerra, M. / Colizzi, F. / Mayor-Ruiz, C. / Biondi, R.M. / Soliva, R. / Macias, M.J. / Orozco, M. / Nebreda, A.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pvu.cif.gz | 367.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pvu.ent.gz | 234.2 KB | Display | PDB format |
PDBx/mmJSON format | 7pvu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pvu_validation.pdf.gz | 714.2 KB | Display | wwPDB validaton report |
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Full document | 7pvu_full_validation.pdf.gz | 718.9 KB | Display | |
Data in XML | 7pvu_validation.xml.gz | 26.6 KB | Display | |
Data in CIF | 7pvu_validation.cif.gz | 37.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pv/7pvu ftp://data.pdbj.org/pub/pdb/validation_reports/pv/7pvu | HTTPS FTP |
-Related structure data
Related structure data | 7z6iC 7z9tC 3queS 7pv3 7q1a S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 41235.020 Da / Num. of mol.: 2 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 #2: Chemical | ChemComp-8DI / | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.3 Å3/Da / Density % sol: 46.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8 / Details: 27% PEG 3350, 0,1M BIS-TRIS pH 6.8 / Temp details: RT |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Oxford Cryosystems 700 / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2020 / Details: Eliptically bent mirror |
Radiation | Monochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→79.702 Å / Num. obs: 44958 / % possible obs: 100 % / Redundancy: 5.8 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.82→1.92 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 4938 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3que Resolution: 2.154→79.702 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.284 / WRfactor Rwork: 0.224 / SU B: 12.974 / SU ML: 0.163 / Average fsc free: 0.9551 / Average fsc work: 0.9687 / Cross valid method: THROUGHOUT / ESU R: 0.283 / ESU R Free: 0.206 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.897 Å2
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Refinement step | Cycle: LAST / Resolution: 2.154→79.702 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / 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 | Selection: ALL |