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Yorodumi- PDB-6emh: Crystal structure of JNK3 in complex with a pyridinylimidazole in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6emh | ||||||
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Title | Crystal structure of JNK3 in complex with a pyridinylimidazole inhibitor | ||||||
Components | Mitogen-activated protein kinase 10 | ||||||
Keywords | TRANSFERASE / Protein Kinase Activity Map Kinase Activity ATP Binding Protein Phosphorylation | ||||||
Function / homology | Function and homology information JUN kinase activity / Activation of the AP-1 family of transcription factors / Fc-epsilon receptor signaling pathway / MAP kinase kinase activity / response to light stimulus / mitogen-activated protein kinase / JNK cascade / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / FCERI mediated MAPK activation / regulation of circadian rhythm ...JUN kinase activity / Activation of the AP-1 family of transcription factors / Fc-epsilon receptor signaling pathway / MAP kinase kinase activity / response to light stimulus / mitogen-activated protein kinase / JNK cascade / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / FCERI mediated MAPK activation / regulation of circadian rhythm / cellular senescence / rhythmic process / Oxidative Stress Induced Senescence / protein phosphorylation / protein serine kinase activity / signal transduction / mitochondrion / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å | ||||||
Authors | Macedo, J.T. / Stehle, T. / Blaum, B.S. | ||||||
Citation | Journal: ACS Omega / Year: 2018 Title: Structural Optimization of a Pyridinylimidazole Scaffold: Shifting the Selectivity from p38 alpha Mitogen-Activated Protein Kinase to c-Jun N-Terminal Kinase 3. Authors: Ansideri, F. / Macedo, J.T. / Eitel, M. / El-Gokha, A. / Zinad, D.S. / Scarpellini, C. / Kudolo, M. / Schollmeyer, D. / Boeckler, F.M. / Blaum, B.S. / Laufer, S.A. / Koch, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6emh.cif.gz | 586.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6emh.ent.gz | 483.2 KB | Display | PDB format |
PDBx/mmJSON format | 6emh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/em/6emh ftp://data.pdbj.org/pub/pdb/validation_reports/em/6emh | HTTPS FTP |
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-Related structure data
Related structure data | 6ekdC 6eq9C 4x21S 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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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 42260.855 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK10, JNK3, JNK3A, PRKM10, SAPK1B / Production host: Escherichia coli (E. coli) References: UniProt: P53779, mitogen-activated protein kinase |
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-Non-polymers , 8 types, 883 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-BGE / #5: Chemical | ChemComp-EDO / #6: Chemical | #7: Chemical | #8: Chemical | #9: Water | ChemComp-HOH / | |
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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: 2.36 Å3/Da / Density % sol: 47.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100 mM Bis-Tris pH5.5, 200 mM NaCl, 29% PEG 3350, 1mM AMP-PCP, 0.4 mM Zwittergent 3-14, 10% Ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.9 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→50 Å / Num. obs: 157963 / % possible obs: 99.9 % / Redundancy: 26.4 % / Rrim(I) all: 0.089 / Net I/σ(I): 22.98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4X21 Resolution: 1.76→48.01 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / Cross valid method: FREE R-VALUE / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS /
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Displacement parameters |
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Refinement step | Cycle: 1 / Resolution: 1.76→48.01 Å
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Refine LS restraints |
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