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- PDB-6ekd: Crystal structure of JNK3 in complex with a pyridinylimidazole in... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ekd | ||||||
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Title | Crystal structure of JNK3 in complex with a pyridinylimidazole inhibitor | ||||||
![]() | Mitogen-activated protein kinase 10 | ||||||
![]() | TRANSFERASE / Protein Kinase Activity Map Kinase Activity ATP Binding Protein Phosphorylation | ||||||
Function / homology | ![]() 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Macedo, J.T. / Stehle, T. / Blaum, B.S. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 149.3 KB | Display | ![]() |
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PDB format | ![]() | 115 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 759 KB | Display | ![]() |
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Full document | ![]() | 760.6 KB | Display | |
Data in XML | ![]() | 14.7 KB | Display | |
Data in CIF | ![]() | 20.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6emhC ![]() 6eq9C ![]() 4x21S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 42260.855 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P53779, mitogen-activated protein kinase |
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#2: Chemical | ChemComp-BME / |
#3: Chemical | ChemComp-EDO / |
#4: Chemical | ChemComp-B9K / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 100 mM Bis Tris pH 5.5, 200 mM NaCl, 29% PEG 3350, 1 mM 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: ![]() ![]() ![]() |
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 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 20913 / % possible obs: 100 % / Redundancy: 25.8 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 26.4 |
Reflection shell | Resolution: 2.1→2.15 Å / Rmerge(I) obs: 2.982 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4X21 Resolution: 2.1→48.48 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.928 / SU B: 13.325 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.239 / ESU R Free: 0.204 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.355 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→48.48 Å
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Refine LS restraints |
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