+Open data
-Basic information
Entry | Database: PDB / ID: 3gok | ||||||
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Title | Binding site mapping of protein ligands | ||||||
Components | MAP kinase-activated protein kinase 2 | ||||||
Keywords | TRANSFERASE / MK2 / MAPKAP kinase 2 / Isotope labelling / insect cell expression / ATP-binding / Kinase / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Scheich, C. | ||||||
Citation | Journal: To be published Title: Binding site mapping of protein ligands Authors: Scheich, C. / Smith, M.A. / Barker, J.D. / Kahmann, J. / Hesterkamp, T. / Schade, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gok.cif.gz | 695.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gok.ent.gz | 577.8 KB | Display | PDB format |
PDBx/mmJSON format | 3gok.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gok_validation.pdf.gz | 3.1 MB | Display | wwPDB validaton report |
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Full document | 3gok_full_validation.pdf.gz | 3.2 MB | Display | |
Data in XML | 3gok_validation.xml.gz | 125.8 KB | Display | |
Data in CIF | 3gok_validation.cif.gz | 165.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/go/3gok ftp://data.pdbj.org/pub/pdb/validation_reports/go/3gok | HTTPS FTP |
-Related structure data
Related structure data | 2jbpS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
-Components
#1: Protein | Mass: 38328.238 Da / Num. of mol.: 12 / Fragment: Protein kinase domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: 9261, MAPKAPK2 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf21 References: UniProt: P49137, non-specific serine/threonine protein kinase #2: Chemical | ChemComp-P4O / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.52 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 40% ethanol, 5% PEG1000, 100mM phosphate-citrate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 273K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.972 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 1, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→46.73 Å / Num. all: 129778 / Num. obs: 91154 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.02 % / Rmerge(I) obs: 0.173 / Rsym value: 0.173 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 3.99 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.2 / Rsym value: 0.012 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2JBP Resolution: 3.2→46.73 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.909 / SU B: 52.631 / SU ML: 0.387 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.477 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.458 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→46.73 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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