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Yorodumi- PDB-5b2k: A crucial role of Cys218 in the stabilization of an unprecedented... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5b2k | ||||||
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Title | A crucial role of Cys218 in the stabilization of an unprecedented auto-inhibition form of MAP2K7 | ||||||
Components | Dual specificity mitogen-activated protein kinase kinase 7 | ||||||
Keywords | TRANSFERASE / protein kinase / Apo structure / auto-inhibition form | ||||||
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 / magnesium ion binding / enzyme binding / signal transduction / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Sogabe, Y. / Hashimoto, T. / Matsumoto, T. / Kirii, Y. / Sawa, M. / Kinoshita, T. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2016 Title: A crucial role of Cys218 in configuring an unprecedented auto-inhibition form of MAP2K7 Authors: Sogabe, Y. / Hashimoto, T. / Matsumoto, T. / Kirii, Y. / Sawa, M. / Kinoshita, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5b2k.cif.gz | 68.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b2k.ent.gz | 48.6 KB | Display | PDB format |
PDBx/mmJSON format | 5b2k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b2/5b2k ftp://data.pdbj.org/pub/pdb/validation_reports/b2/5b2k | HTTPS FTP |
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-Related structure data
Related structure data | 5b2lC 5b2mC 3wzuS 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: 36998.902 Da / Num. of mol.: 1 / Fragment: UNP residues 103-419 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 (E. coli) References: UniProt: O14733, mitogen-activated protein kinase kinase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.78 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 3350, sodium citrate tribasic, Hepes |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jun 30, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→50 Å / Num. obs: 11135 / % possible obs: 95 % / Redundancy: 13.9 % / Net I/σ(I): 22.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WZU Resolution: 2.75→44.96 Å / Cor.coef. Fo:Fc: 0.866 / Cor.coef. Fo:Fc free: 0.778 / Cross valid method: THROUGHOUT / ESU R: 1.239 / ESU R Free: 0.455 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 45.804 Å2
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Refinement step | Cycle: LAST / Resolution: 2.75→44.96 Å
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Refine LS restraints |
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