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- PDB-7ovm: Protein kinase MKK7 in complex with cyclobutyl-substituted indazole -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ovm | ||||||
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Title | Protein kinase MKK7 in complex with cyclobutyl-substituted indazole | ||||||
![]() | Dual specificity mitogen-activated protein kinase kinase 7 | ||||||
![]() | TRANSFERASE / Inhibitor / Complex / MKK7 / Kinase / Triazole / Click-Chemistry / CuACC | ||||||
Function / homology | ![]() 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 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Buehrmann, M. / Wiese, J.N. / Mueller, M.P. / Rauh, D. | ||||||
![]() | ![]() Title: Optimization of Covalent MKK7 Inhibitors via Crude Nanomole-Scale Libraries. Authors: Gehrtz, P. / Marom, S. / Buhrmann, M. / Hardick, J. / Kleinbolting, S. / Shraga, A. / Dubiella, C. / Gabizon, R. / Wiese, J.N. / Muller, M.P. / Cohen, G. / Babaev, I. / Shurrush, K. / Avram, ...Authors: Gehrtz, P. / Marom, S. / Buhrmann, M. / Hardick, J. / Kleinbolting, S. / Shraga, A. / Dubiella, C. / Gabizon, R. / Wiese, J.N. / Muller, M.P. / Cohen, G. / Babaev, I. / Shurrush, K. / Avram, L. / Resnick, E. / Barr, H. / Rauh, D. / London, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 151 KB | Display | ![]() |
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PDB format | ![]() | 98 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 722 KB | Display | ![]() |
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Full document | ![]() | 723.6 KB | Display | |
Data in XML | ![]() | 12 KB | Display | |
Data in CIF | ![]() | 15.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7oviC ![]() 7ovjC ![]() 7ovkC ![]() 7ovlC ![]() 7ovnC ![]() 6qflS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() References: UniProt: O14733, mitogen-activated protein kinase kinase |
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#2: Chemical | ChemComp-21I / ~{ |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.38 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 180-220 mM sodium citrate, 15-25 % PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 20, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9197 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 8219 / % possible obs: 100 % / Redundancy: 13.14 % / Biso Wilson estimate: 83.37 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.11 / Net I/σ(I): 17.65 |
Reflection shell | Resolution: 2.9→3 Å / Mean I/σ(I) obs: 2.18 / Num. unique obs: 763 / CC1/2: 0.81 / Rrim(I) all: 1.449 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6QFL Resolution: 2.9→49.19 Å / SU ML: 0.591 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.7919 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 85.27 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→49.19 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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