+Open data
-Basic information
Entry | Database: PDB / ID: 6y82 | |||||||||
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Title | Fragment KCL_804 in complex with MAP kinase p38-alpha | |||||||||
Components | Mitogen-activated protein kinase 14MAPK14 | |||||||||
Keywords | TRANSFERASE / FBDD / FRAGMENT BASED DRUG DESIGN / P38 / MAPK14 / KINASE | |||||||||
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 / 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 / lipopolysaccharide-mediated signaling pathway / positive regulation of cardiac muscle cell proliferation / striated muscle cell differentiation / response to muscle stretch / positive regulation of brown fat cell differentiation / Neutrophil degranulation / positive regulation of interleukin-12 production / osteoclast differentiation / positive regulation of erythrocyte differentiation / DNA damage checkpoint signaling / cellular response to ionizing radiation / stem cell differentiation / positive regulation of glucose import / placenta development / 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 / angiogenesis / cellular response to lipopolysaccharide / response to lipopolysaccharide / transcription by RNA polymerase II / protein kinase activity / intracellular signal transduction / nuclear speck / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / apoptotic process / DNA damage response / regulation of DNA-templated transcription / positive regulation of gene expression / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å | |||||||||
Authors | De Nicola, G.F. / Nichols, C.E. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: To Be Published Title: Fragment KCL_804 in complex with MAP kinase p38-alpha Authors: De Nicola, G.F. / Nichols, C.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6y82.cif.gz | 112.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6y82.ent.gz | 68.6 KB | Display | PDB format |
PDBx/mmJSON format | 6y82.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y8/6y82 ftp://data.pdbj.org/pub/pdb/validation_reports/y8/6y82 | HTTPS FTP |
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-Related structure data
Related structure data | 6sovS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 41322.098 Da / Num. of mol.: 1 / Mutation: C162S 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-SB4 / | ||||||
#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-308 / ( | #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: 2.58 Å3/Da / Density % sol: 52.28 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 15% PEG400, 5% PEG550-MME, 0.1M CALCIUM ACETATE, 0.1M MES PH6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 1.44→63.62 Å / Num. obs: 74917 / % possible obs: 96.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 15.16 Å2 / CC1/2: 1 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.44→1.46 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3677 / CC1/2: 0.6 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6SOV Resolution: 1.44→39.98 Å / SU ML: 0.2046 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.355
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.24 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.44→39.98 Å
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Refine LS restraints |
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LS refinement shell |
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