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Yorodumi- PDB-4u79: Crystal structure of human JNK3 in complex with a benzenesulfonam... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4u79 | ||||||
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Title | Crystal structure of human JNK3 in complex with a benzenesulfonamide inhibitor. | ||||||
Components | Mitogen-activated protein kinase 10 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Transferase / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
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: 2.23 Å | ||||||
Authors | Mohr, C. | ||||||
Citation | Journal: Acs Med.Chem.Lett. / Year: 2015 Title: Unfolded Protein Response in Cancer: IRE1 alpha Inhibition by Selective Kinase Ligands Does Not Impair Tumor Cell Viability. Authors: Harrington, P.E. / Biswas, K. / Malwitz, D. / Tasker, A.S. / Mohr, C. / Andrews, K.L. / Dellamaggiore, K. / Kendall, R. / Beckmann, H. / Jaeckel, P. / Materna-Reichelt, S. / Allen, J.R. / Lipford, J.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4u79.cif.gz | 152.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4u79.ent.gz | 119 KB | Display | PDB format |
PDBx/mmJSON format | 4u79.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4u79_validation.pdf.gz | 703.7 KB | Display | wwPDB validaton report |
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Full document | 4u79_full_validation.pdf.gz | 709.3 KB | Display | |
Data in XML | 4u79_validation.xml.gz | 15 KB | Display | |
Data in CIF | 4u79_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u7/4u79 ftp://data.pdbj.org/pub/pdb/validation_reports/u7/4u79 | HTTPS FTP |
-Related structure data
Related structure data | 4u6rC 3da6S C: citing same article (ref.) 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
#1: Protein | Mass: 42059.676 Da / Num. of mol.: 1 / Fragment: UNP residues 39-402 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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#2: Chemical | ChemComp-3EL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.67 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES, 20mMBMe, 30%PEG550MME, pH7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 30, 2011 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.23→50 Å / Num. obs: 21261 / % possible obs: 99.9 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 12.18 |
Reflection shell | Resolution: 2.23→2.3 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.558 / Mean I/σ(I) obs: 2.04 / % possible all: 99.9 |
-Processing
Software | Name: REFMAC / Version: 5.8.0071 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DA6 Resolution: 2.23→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.94 / SU B: 19.089 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R: 0.278 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.958 Å2
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Refinement step | Cycle: 1 / Resolution: 2.23→50 Å
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