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Yorodumi- PDB-6yg3: Crystal structure of MKK7 (MAP2K7) covalently bound with CPT1-70-1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6yg3 | ||||||
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Title | Crystal structure of MKK7 (MAP2K7) covalently bound with CPT1-70-1 | ||||||
Components | Dual specificity mitogen-activated protein kinase kinase 7 | ||||||
Keywords | TRANSFERASE / kinase / kinase inhibitor / MKK7 / MEK7 / MAP2K7 / MAP2K / MEK / JNK signaling / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
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 / response to UV / stress-activated MAPK cascade / 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 / cellular response to lipopolysaccharide / protein phosphatase binding / protein tyrosine kinase activity / Oxidative Stress Induced Senescence / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Chaikuad, A. / Tan, L. / Wang, J. / Liang, Y. / Gray, N.S. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Cell Chem Biol / Year: 2020 Title: Catalytic Domain Plasticity of MKK7 Reveals Structural Mechanisms of Allosteric Activation and Diverse Targeting Opportunities. Authors: Schroder, M. / Tan, L. / Wang, J. / Liang, Y. / Gray, N.S. / Knapp, S. / Chaikuad, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yg3.cif.gz | 127.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yg3.ent.gz | 96.4 KB | Display | PDB format |
PDBx/mmJSON format | 6yg3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yg3_validation.pdf.gz | 754.9 KB | Display | wwPDB validaton report |
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Full document | 6yg3_full_validation.pdf.gz | 757.7 KB | Display | |
Data in XML | 6yg3_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 6yg3_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yg/6yg3 ftp://data.pdbj.org/pub/pdb/validation_reports/yg/6yg3 | HTTPS FTP |
-Related structure data
Related structure data | 6yfzC 6yg0C 6yg1C 6yg2C 6yg4C 6yg5C 6yg6C 6yg7C 6yz4C 2dylS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34944.621 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: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -R3-pRARE2 References: UniProt: O14733, mitogen-activated protein kinase kinase | ||||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-6HF / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.4 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.2 Details: 19% PEG3350, 0.25 M ammonium acetate, 0.1 M tris, pH 8.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 13, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.05→30.385 Å / Num. obs: 20596 / % possible obs: 99.1 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.041 / Rrim(I) all: 0.107 / Net I/av σ(I): 5.9 / Net I/σ(I): 10.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2dyl Resolution: 2.05→30.38 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.938 / SU B: 10.942 / SU ML: 0.145 / SU R Cruickshank DPI: 0.1869 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.187 / ESU R Free: 0.169 Details: U VALUES : WITH TLS ADDED 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 max: 109.27 Å2 / Biso mean: 44.495 Å2 / Biso min: 25.2 Å2
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Refinement step | Cycle: final / Resolution: 2.05→30.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | S22: 0.0259 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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