[English] 日本語
Yorodumi- PDB-3she: Novel ATP-competitive MK2 inhibitors with potent biochemical and ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3she | ||||||
---|---|---|---|---|---|---|---|
Title | Novel ATP-competitive MK2 inhibitors with potent biochemical and cell-based activity throughout the series | ||||||
Components | MAP kinase-activated protein kinase 3 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Kinase domain with bound inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information macropinocytosis / calcium-dependent protein serine/threonine kinase activity / calmodulin-dependent protein kinase activity / mitogen-activated protein kinase binding / toll-like receptor signaling pathway / MAP kinase kinase activity / vascular endothelial growth factor receptor signaling pathway / p38MAPK events / response to cytokine / activated TAK1 mediates p38 MAPK activation ...macropinocytosis / calcium-dependent protein serine/threonine kinase activity / calmodulin-dependent protein kinase activity / mitogen-activated protein kinase binding / toll-like receptor signaling pathway / MAP kinase kinase activity / vascular endothelial growth factor receptor signaling pathway / p38MAPK events / response to cytokine / activated TAK1 mediates p38 MAPK activation / VEGFA-VEGFR2 Pathway / peptidyl-serine phosphorylation / Oxidative Stress Induced Senescence / response to lipopolysaccharide / calmodulin binding / non-specific serine/threonine protein kinase / intracellular signal transduction / protein serine kinase activity / protein serine/threonine kinase activity / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Oubrie, A. / Kazemier, B. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2012 Title: Novel ATP competitive MK2 inhibitors with potent biochemical and cell-based activity throughout the series. Authors: Oubrie, A. / Kaptein, A. / de Zwart, E. / Hoogenboom, N. / Goorden, R. / van de Kar, B. / van Hoek, M. / de Kimpe, V. / van der Heijden, R. / Borsboom, J. / Kazemier, B. / de Roos, J. / ...Authors: Oubrie, A. / Kaptein, A. / de Zwart, E. / Hoogenboom, N. / Goorden, R. / van de Kar, B. / van Hoek, M. / de Kimpe, V. / van der Heijden, R. / Borsboom, J. / Kazemier, B. / de Roos, J. / Scheffers, M. / Lommerse, J. / Schultz-Fademrecht, C. / Barf, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3she.cif.gz | 128.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3she.ent.gz | 100.7 KB | Display | PDB format |
PDBx/mmJSON format | 3she.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sh/3she ftp://data.pdbj.org/pub/pdb/validation_reports/sh/3she | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 36428.602 Da / Num. of mol.: 1 / Fragment: Kinase domain (UNP residues 33-349) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAPKAPK3 / Plasmid: pTrilJ-POPIN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q16644, non-specific serine/threonine protein kinase |
---|---|
#2: Chemical | ChemComp-I85 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.37 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.1 M citrate/Bis-tris propane, 12% PEG3350, 10 mM DTT, 1 mM inhibitor, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 16, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→44.6 Å / Num. all: 17325 / Num. obs: 17325 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.062 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 1712 / Rsym value: 0.446 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→27.08 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.926 / SU B: 19.92 / SU ML: 0.229 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.318 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 83.16 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→27.08 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.25→2.308 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|