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Yorodumi- PDB-2jbo: Protein kinase MK2 in complex with an inhibitor (crystal form-1, ... -
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-Basic information
Entry | Database: PDB / ID: 2jbo | ||||||
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Title | Protein kinase MK2 in complex with an inhibitor (crystal form-1, soaking) | ||||||
Components | MAP KINASE-ACTIVATED PROTEIN KINASE 2 | ||||||
Keywords | TRANSFERASE / SER-THR KINASE / MAPKAP KINASE 2 / PHOSPHORYLATION / MK2 / KINASE / ATP SITE / ATP-BINDING / SERINE/THREONINE-PROTEIN KINASE / SMALL MOLECULE INHIBITOR / NUCLEOTIDE-BINDING | ||||||
Function / homology | Function and homology information macropinocytosis / CREB phosphorylation / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / leukotriene metabolic process / Synthesis of Leukotrienes (LT) and Eoxins (EX) / calcium-dependent protein serine/threonine kinase activity / regulation of tumor necrosis factor production / regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of macrophage cytokine production ...macropinocytosis / CREB phosphorylation / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / leukotriene metabolic process / Synthesis of Leukotrienes (LT) and Eoxins (EX) / calcium-dependent protein serine/threonine kinase activity / regulation of tumor necrosis factor production / regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of macrophage cytokine production / mitogen-activated protein kinase binding / regulation of interleukin-6 production / calcium/calmodulin-dependent protein kinase activity / 3'-UTR-mediated mRNA stabilization / toll-like receptor signaling pathway / p38MAPK cascade / inner ear development / Regulation of HSF1-mediated heat shock response / cellular response to vascular endothelial growth factor stimulus / vascular endothelial growth factor receptor signaling pathway / regulation of cellular response to heat / p38MAPK events / regulation of mRNA stability / response to cytokine / activated TAK1 mediates p38 MAPK activation / Regulation of TNFR1 signaling / VEGFA-VEGFR2 Pathway / positive regulation of tumor necrosis factor production / MAPK cascade / peptidyl-serine phosphorylation / Oxidative Stress Induced Senescence / response to lipopolysaccharide / non-specific serine/threonine protein kinase / calmodulin binding / protein kinase activity / intracellular signal transduction / inflammatory response / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / DNA damage response / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.1 Å | ||||||
Authors | Hillig, R.C. / Eberspaecher, U. / Monteclaro, F. / Huber, M. / Nguyen, D. / Mengel, A. / Muller-Tiemann, B. / Egner, U. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Structural Basis for a High Affinity Inhibitor Bound to Protein Kinase Mk2. Authors: Hillig, R.C. / Eberspaecher, U. / Monteclaro, F. / Huber, M. / Nguyen, D. / Mengel, A. / Muller-Tiemann, B. / Egner, U. #1: Journal: Protein Sci. / Year: 2006 Title: Identifying Protein Construct Variants with Increased Crystallization Propensity--A Case Study. Authors: Malawski, G.A. / Hillig, R.C. / Monteclaro, F. / Eberspaecher, U. / Schmitz, A.A. / Crusius, K. / Huber, M. / Egner, U. / Donner, P. / Muller-Tiemann, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jbo.cif.gz | 76.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jbo.ent.gz | 58 KB | Display | PDB format |
PDBx/mmJSON format | 2jbo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jbo_validation.pdf.gz | 697.3 KB | Display | wwPDB validaton report |
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Full document | 2jbo_full_validation.pdf.gz | 706.3 KB | Display | |
Data in XML | 2jbo_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 2jbo_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/2jbo ftp://data.pdbj.org/pub/pdb/validation_reports/jb/2jbo | HTTPS FTP |
-Related structure data
Related structure data | 2jbpC 1ny3S 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: 37665.461 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 41-364 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: P49137, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-P4O / |
#4: Water | ChemComp-HOH / |
Sequence details | N-TERMINAL RESIDUES GLY-SER ARE CLONING ARTIFACTS FROM A THROMBIN CLEAVAGE SITE AFTER GST TAG REMOVAL |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.5 Å3/Da / Density % sol: 72.9 % / Description: NONE |
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Crystal grow | pH: 4.5 Details: 1.5-1.6M SODIUM POTASSIUM PHOSPHATE PH 4.5, 0.014M DEOXY-BIGCHAP. THE INHIBITOR WAS SOAKED INTO CRYSTALS GROWN INITIALLY FROM MK2-ADP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99991 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 21, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99991 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→48.9 Å / Num. obs: 13232 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 87.6 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 27.1 |
Reflection shell | Resolution: 3.1→3.15 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1NY3 Resolution: 3.1→48.9 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.866 / SU B: 28.333 / SU ML: 0.249 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.679 / ESU R Free: 0.382 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 72.47 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→48.9 Å
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