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Yorodumi- PDB-5n66: Crystal Structure of p38alpha in Complex with Lipid Pocket Ligand 9j -
+Open data
-Basic information
Entry | Database: PDB / ID: 5n66 | ||||||
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Title | Crystal Structure of p38alpha in Complex with Lipid Pocket Ligand 9j | ||||||
Components | Mitogen-activated protein kinase 14MAPK14 | ||||||
Keywords | TRANSFERASE / kinase / small molecule / lipid pocket / p38 / quinazoline | ||||||
Function / homology | Function and homology information 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 / DSCAM interactions / cartilage condensation ...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 / DSCAM interactions / cartilage condensation / cellular response to UV-B / Platelet sensitization by LDL / stress-activated protein kinase signaling cascade / mitogen-activated protein kinase p38 binding / positive regulation of myoblast fusion / positive regulation of muscle cell differentiation / negative regulation of hippo signaling / positive regulation of myotube differentiation / NFAT protein binding / Myogenesis / glucose import / response to dietary excess / Activation of the AP-1 family of transcription factors / ERK/MAPK targets / regulation of cytokine production involved in inflammatory response / p38MAPK cascade / fatty acid oxidation / cellular response to lipoteichoic acid / MAP kinase kinase activity / response to muramyl dipeptide / RHO GTPases Activate NADPH Oxidases / regulation of ossification / MAP kinase activity / mitogen-activated protein kinase / cellular response to vascular endothelial growth factor stimulus / positive regulation of myoblast differentiation / chondrocyte differentiation / vascular endothelial growth factor receptor signaling pathway / stress-activated MAPK cascade / skeletal muscle tissue development / signal transduction in response to DNA damage / lipopolysaccharide-mediated signaling pathway / negative regulation of inflammatory response to antigenic stimulus / positive regulation of cardiac muscle cell proliferation / p38MAPK events / striated muscle cell differentiation / response to muscle stretch / positive regulation of brown fat cell differentiation / positive regulation of interleukin-12 production / osteoclast differentiation / positive regulation of erythrocyte differentiation / placenta development / DNA damage checkpoint signaling / activated TAK1 mediates p38 MAPK activation / cellular response to ionizing radiation / stem cell differentiation / positive regulation of glucose import / negative regulation of canonical Wnt signaling pathway / response to insulin / NOD1/2 Signaling Pathway / bone development / cell morphogenesis / platelet activation / osteoblast differentiation / cellular response to virus / VEGFA-VEGFR2 Pathway / spindle pole / positive regulation of protein import into nucleus / ADP signalling through P2Y purinoceptor 1 / glucose metabolic process / positive regulation of reactive oxygen species metabolic process / chemotaxis / cellular senescence / cellular response to tumor necrosis factor / protein phosphatase binding / peptidyl-serine phosphorylation / angiogenesis / Oxidative Stress Induced Senescence / secretory granule lumen / cellular response to lipopolysaccharide / 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 / SYNCHROTRON / Resolution: 2.4 Å | ||||||
Authors | Buehrmann, M. / Mueller, M.P. / Wiedemann, B. / Rauh, D. | ||||||
Funding support | Germany, 1items
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Citation | Journal: PLoS ONE / Year: 2017 Title: Structure-based design, synthesis and crystallization of 2-arylquinazolines as lipid pocket ligands of p38 alpha MAPK. Authors: Buhrmann, M. / Wiedemann, B.M. / Muller, M.P. / Hardick, J. / Ecke, M. / Rauh, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5n66.cif.gz | 150.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n66.ent.gz | 117.9 KB | Display | PDB format |
PDBx/mmJSON format | 5n66.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n6/5n66 ftp://data.pdbj.org/pub/pdb/validation_reports/n6/5n66 | HTTPS FTP |
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-Related structure data
Related structure data | 5n63C 5n64C 5n65C 5n67C 5n68C 4dliS 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: 41343.195 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, SAPK2A / Production host: Escherichia coli (E. coli) References: UniProt: Q16539, mitogen-activated protein kinase |
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#2: Chemical | ChemComp-BW1 / ~{ |
#3: Chemical | ChemComp-B96 / |
#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: 2.39 Å3/Da / Density % sol: 48.48 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 100 mM MES pH 5.6-6.2 20-30 % PEG4000 50 mM BOG |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9786 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 15879 / % possible obs: 100 % / Redundancy: 13 % / Rrim(I) all: 0.139 / Net I/σ(I): 11.41 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 13.7 % / Mean I/σ(I) obs: 1.95 / Rrim(I) all: 1.256 / % possible all: 100 |
-Processing
Software |
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Refinement | Starting model: 4DLI Resolution: 2.4→49.565 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 25.88 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→49.565 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -6.8333 Å / Origin y: -4.1227 Å / Origin z: 16.4262 Å
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Refinement TLS group | Selection details: (chain A and resseq 6:353) |