+Open data
-Basic information
Entry | Database: PDB / ID: 5z1e | ||||||
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Title | MAP2K7 C218S mutant-inhibitor | ||||||
Components | Dual specificity mitogen-activated protein kinase kinase 7 | ||||||
Keywords | TRANSFERASE / protein 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 / 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: 2.3 Å | ||||||
Authors | Kinoshita, T. / London, N. | ||||||
Citation | Journal: Cell Chem Biol / Year: 2019 Title: Covalent Docking Identifies a Potent and Selective MKK7 Inhibitor. Authors: Shraga, A. / Olshvang, E. / Davidzohn, N. / Khoshkenar, P. / Germain, N. / Shurrush, K. / Carvalho, S. / Avram, L. / Albeck, S. / Unger, T. / Lefker, B. / Subramanyam, C. / Hudkins, R.L. / ...Authors: Shraga, A. / Olshvang, E. / Davidzohn, N. / Khoshkenar, P. / Germain, N. / Shurrush, K. / Carvalho, S. / Avram, L. / Albeck, S. / Unger, T. / Lefker, B. / Subramanyam, C. / Hudkins, R.L. / Mitchell, A. / Shulman, Z. / Kinoshita, T. / London, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5z1e.cif.gz | 78.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z1e.ent.gz | 55.6 KB | Display | PDB format |
PDBx/mmJSON format | 5z1e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5z1e_validation.pdf.gz | 716.9 KB | Display | wwPDB validaton report |
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Full document | 5z1e_full_validation.pdf.gz | 719.4 KB | Display | |
Data in XML | 5z1e_validation.xml.gz | 14 KB | Display | |
Data in CIF | 5z1e_validation.cif.gz | 19.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z1/5z1e ftp://data.pdbj.org/pub/pdb/validation_reports/z1/5z1e | HTTPS FTP |
-Related structure data
Related structure data | 5z1dC 5y90S 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: 36982.836 Da / Num. of mol.: 1 / Fragment: UNP residues 103-419 / Mutation: C218S 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 B (bacteria) References: UniProt: O14733, mitogen-activated protein kinase kinase |
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#2: Chemical | ChemComp-95U / |
#3: Water | ChemComp-HOH / |
Sequence details | Authors state that the conflict(SER,218A) is due to the expression artifact. (see SEQADV) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.6 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, sodium citrate |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: AichiSR / Beamline: BL2S1 / Wavelength: 1.12 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 6, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→46.6 Å / Num. obs: 16329 / % possible obs: 99.8 % / Redundancy: 6.9 % / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.3→2.44 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5Y90 Resolution: 2.3→46.6 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.894 / SU B: 8.479 / SU ML: 0.2 / Cross valid method: THROUGHOUT / ESU R: 0.307 / ESU R Free: 0.267 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.195 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→46.6 Å
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Refine LS restraints |
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