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Yorodumi- PDB-6ib2: The structure of MKK7 in complex with the covalent 4-amino-pyrazo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ib2 | ||||||
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Title | The structure of MKK7 in complex with the covalent 4-amino-pyrazolopyrimidine 4a | ||||||
Components | Dual specificity mitogen-activated protein kinase kinase 7 | ||||||
Keywords | TRANSFERASE / MKK7 / Inhibitor / Covalent / JNK / Kinase | ||||||
Function / homology | Function and homology information JUN kinase kinase activity / regulation of motor neuron apoptotic process / mitogen-activated protein kinase kinase / response to osmotic stress / Fc-epsilon receptor signaling pathway / positive regulation of telomere capping / MAP kinase kinase activity / Uptake and function of anthrax toxins / MAP kinase activity / cellular response to interleukin-1 ...JUN kinase kinase activity / regulation of motor neuron apoptotic process / mitogen-activated protein kinase kinase / response to osmotic stress / Fc-epsilon receptor signaling pathway / positive regulation of telomere capping / MAP kinase kinase activity / Uptake and function of anthrax toxins / MAP kinase activity / cellular response to interleukin-1 / response to tumor necrosis factor / stress-activated MAPK cascade / response to UV / positive regulation of JUN kinase activity / JNK cascade / positive regulation of telomerase activity / positive regulation of telomere maintenance via telomerase / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / molecular function activator activity / FCERI mediated MAPK activation / positive regulation of JNK cascade / response to wounding / cellular senescence / response to heat / protein phosphatase binding / protein tyrosine kinase activity / Oxidative Stress Induced Senescence / cellular response to lipopolysaccharide / positive regulation of ERK1 and ERK2 cascade / phosphorylation / protein serine kinase activity / apoptotic process / protein kinase binding / positive regulation of DNA-templated transcription / enzyme binding / magnesium ion binding / signal transduction / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Wolle, P. / Hardick, J. / Mueller, M.P. / Rauh, D. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2019 Title: Targeting the MKK7-JNK (Mitogen-Activated Protein Kinase Kinase 7-c-Jun N-Terminal Kinase) Pathway with Covalent Inhibitors. Authors: Wolle, P. / Hardick, J. / Cronin, S.J.F. / Engel, J. / Baumann, M. / Lategahn, J. / Penninger, J.M. / Rauh, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ib2.cif.gz | 71.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ib2.ent.gz | 50.2 KB | Display | PDB format |
PDBx/mmJSON format | 6ib2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ib/6ib2 ftp://data.pdbj.org/pub/pdb/validation_reports/ib/6ib2 | HTTPS FTP |
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-Related structure data
Related structure data | 6ib0C 2dylS 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: 36161.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAP2K7, JNKK2, MEK7, MKK7, PRKMK7, SKK4 / Plasmid: pet41b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 References: UniProt: O14733, mitogen-activated protein kinase kinase |
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#2: Chemical | ChemComp-862 / |
#3: 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: 2.41 Å3/Da / Density % sol: 48.99 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Sodiumcitrate 20 % PEG3500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99992 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99992 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→45.401 Å / Num. obs: 21038 / % possible obs: 100 % / Redundancy: 12.71 % / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rrim(I) all: 0.097 / Net I/σ(I): 17.33 |
Reflection shell | Resolution: 2.1→2.2 Å / Rmerge(I) obs: 0.793 / Mean I/σ(I) obs: 3.42 / CC1/2: 0.245 / Rrim(I) all: 0.825 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2dyl Resolution: 2.1→45.401 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 26.57 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→45.401 Å
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Refine LS restraints |
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LS refinement shell |
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