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Yorodumi- PDB-6qho: Dual specificity mitogen-activated protein kinase kinase 7 in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qho | ||||||
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Title | Dual specificity mitogen-activated protein kinase kinase 7 in complex with pyrazolopyrimidine 1a | ||||||
Components | Dual specificity mitogen-activated protein kinase kinase 7 | ||||||
Keywords | TRANSFERASE / Protein Kinase / Kinase / MKK7 | ||||||
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 / 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 / cellular response to interleukin-1 / MAP kinase activity / response to tumor necrosis factor / response to UV / stress-activated MAPK cascade / positive regulation of JUN kinase activity / JNK cascade / 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 / cellular response to lipopolysaccharide / protein tyrosine kinase activity / protein phosphatase binding / Oxidative Stress Induced Senescence / positive regulation of ERK1 and ERK2 cascade / 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: 2.7 Å | ||||||
Authors | Wolle, P. / Mueller, M.P. / Rauh, D. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2019 Title: Characterization of Covalent Pyrazolopyrimidine-MKK7 Complexes and a Report on a Unique DFG-in/Leu-in Conformation of Mitogen-Activated Protein Kinase Kinase 7 (MKK7). Authors: Wolle, P. / Engel, J. / Smith, S. / Goebel, L. / Hennes, E. / Lategahn, J. / Rauh, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qho.cif.gz | 68.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qho.ent.gz | 48.1 KB | Display | PDB format |
PDBx/mmJSON format | 6qho.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qho_validation.pdf.gz | 751.5 KB | Display | wwPDB validaton report |
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Full document | 6qho_full_validation.pdf.gz | 752.5 KB | Display | |
Data in XML | 6qho_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 6qho_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qh/6qho ftp://data.pdbj.org/pub/pdb/validation_reports/qh/6qho | HTTPS FTP |
-Related structure data
Related structure data | 6qflC 6qfrC 6qftC 6qg4C 6qg7C 6qhrC 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: 36146.859 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 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: O14733, mitogen-activated protein kinase kinase |
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#2: Chemical | ChemComp-J3H / |
#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: 2.77 Å3/Da / Density % sol: 55.65 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.2 M soidumcitrate 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.91639 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91639 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→49.387 Å / Num. obs: 10088 / % possible obs: 99.4 % / Redundancy: 12.1 % / CC1/2: 0.999 / Rrim(I) all: 0.083 / Rsym value: 0.079 / Net I/σ(I): 21.8 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 10.3 % / Mean I/σ(I) obs: 2.46 / Num. unique obs: 1017 / CC1/2: 0.819 / Rrim(I) all: 0.961 / Rsym value: 0.912 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DYL Resolution: 2.7→49.387 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.97
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→49.387 Å
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Refine LS restraints |
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LS refinement shell |
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