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Yorodumi- PDB-6hwu: Crystal structure of p38alpha in complex with a photoswitchable 2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hwu | |||||||||
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Title | Crystal structure of p38alpha in complex with a photoswitchable 2-Azothiazol-based Inhibitor (compound 2) | |||||||||
Components | Mitogen-activated protein kinase 14 | |||||||||
Keywords | TRANSFERASE / p38alpha / MAPK14 / photoswitchable / Azothiazol | |||||||||
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 / 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 / NFAT protein binding / Myogenesis / glucose import / Activation of the AP-1 family of transcription factors / negative regulation of hippo signaling / 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 / response to dietary excess / 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 / placenta development / activated TAK1 mediates p38 MAPK activation / positive regulation of glucose import / stem cell differentiation / cellular response to ionizing radiation / NOD1/2 Signaling Pathway / response to insulin / bone development / negative regulation of canonical Wnt signaling pathway / cell morphogenesis / cellular senescence / platelet activation / cellular response to virus / spindle pole / VEGFA-VEGFR2 Pathway / 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 response to tumor necrosis factor / peptidyl-serine phosphorylation / protein phosphatase binding / Regulation of TP53 Activity through Phosphorylation / cellular response to lipopolysaccharide / Oxidative Stress Induced Senescence / angiogenesis / secretory granule lumen / 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 / regulation of transcription by RNA polymerase II / Neutrophil degranulation / positive regulation of gene expression / apoptotic process / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular region / nucleoplasm / ATP binding / nucleus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Mueller, M.P. / Rauh, D. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Photochem. Photobiol. Sci. / Year: 2019 Title: 2-Azo-, 2-diazocine-thiazols and 2-azo-imidazoles as photoswitchable kinase inhibitors: limitations and pitfalls of the photoswitchable inhibitor approach. Authors: Schehr, M. / Ianes, C. / Weisner, J. / Heintze, L. / Muller, M.P. / Pichlo, C. / Charl, J. / Brunstein, E. / Ewert, J. / Lehr, M. / Baumann, U. / Rauh, D. / Knippschild, U. / Peifer, C. / Herges, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hwu.cif.gz | 155.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hwu.ent.gz | 120.4 KB | Display | PDB format |
PDBx/mmJSON format | 6hwu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hwu_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6hwu_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6hwu_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 6hwu_validation.cif.gz | 20.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hw/6hwu ftp://data.pdbj.org/pub/pdb/validation_reports/hw/6hwu | HTTPS FTP |
-Related structure data
Related structure data | 6hmpC 6hmrC 6hwtC 6hwvC 5n63S 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: 41494.277 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: Sugar | #3: Chemical | ChemComp-GE5 / | #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: 2.32 Å3/Da / Density % sol: 46.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100 mM MES pH 5.6-6.2, 20-30 % PEG4000, 40mM BOG |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99967 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 22, 2018 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99967 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→49.7 Å / Num. obs: 17697 / % possible obs: 100 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.12 / Rrim(I) all: 0.125 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 13.4 % / Rmerge(I) obs: 1.05 / Mean I/σ(I) obs: 2.3 / Rrim(I) all: 1.09 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5N63 Resolution: 2.3→49.7 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.75
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→49.7 Å
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Refine LS restraints |
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LS refinement shell |
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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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