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- PDB-5cqu: Monoclinic Complex Structure of Protein Kinase CK2 Catalytic Subu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5cqu | |||||||||
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Title | Monoclinic Complex Structure of Protein Kinase CK2 Catalytic Subunit with a Benzotriazole-Based Inhibitor Generated by click-chemistry | |||||||||
![]() | Casein kinase II subunit alpha | |||||||||
![]() | TRANSFERASE / ATP-COMPETITIVE INHIBITOR / Protein kinase CK2 / casein kinase 2 | |||||||||
Function / homology | ![]() regulation of chromosome separation / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Sin3-type complex / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known ...regulation of chromosome separation / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Sin3-type complex / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Maturation of hRSV A proteins / negative regulation of apoptotic signaling pathway / positive regulation of Wnt signaling pathway / negative regulation of double-strand break repair via homologous recombination / chaperone-mediated protein folding / negative regulation of ubiquitin-dependent protein catabolic process / Signal transduction by L1 / peptidyl-threonine phosphorylation / Hsp90 protein binding / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / positive regulation of protein catabolic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / KEAP1-NFE2L2 pathway / double-strand break repair / rhythmic process / kinase activity / positive regulation of cell growth / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / protein stabilization / negative regulation of translation / non-specific serine/threonine protein kinase / regulation of cell cycle / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / DNA damage response / positive regulation of cell population proliferation / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Niefind, K. / Schnitzler, A. / Swider, R. / Maslyk, M. / Ramos, A. | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Synthesis, Biological Activity and Structural Study of New Benzotriazole-Based Protein Kinase CK2 Inhibitors Authors: Swider, R. / Maslyk, M. / Zapico, J.M. / Coderch, C. / Panchuk, R. / Skorokhyd, N. / Schnitzler, A. / Niefind, K. / de Pascual-Teresa, B. / Ramos, A. #1: Journal: Mol. Cell. Biochem. / Year: 2011 Title: MULTISITE-DIRECTED INHIBITORS OF PROTEIN KINASE CK2: NEW CHALLENGES Authors: Swider, R. / Maslyk, M. / Martin-Santamaria, S. / Ramos, A. / de Pascual-Teresa, B. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 155.8 KB | Display | ![]() |
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PDB format | ![]() | 122.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 723 KB | Display | ![]() |
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Full document | ![]() | 726.5 KB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 21.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5cqwC ![]() 2pvrS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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: 40066.742 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P68400, non-specific serine/threonine protein kinase | ||||
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#2: Chemical | ChemComp-JRJ / | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.11 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Protein solution: 6 mg/ml CK2alpha, 0.44 mM AMPPNP, 0.89 mM magnesium chloride, 250 mM NaCl, 12.5 mM Tris/HCl, pH 8.5; Reservoir: 30%(w/v) PEG4000, 0.2 M Lithiumsulfate, 0.1 M Tris/HCL, pH 8. ...Details: Protein solution: 6 mg/ml CK2alpha, 0.44 mM AMPPNP, 0.89 mM magnesium chloride, 250 mM NaCl, 12.5 mM Tris/HCl, pH 8.5; Reservoir: 30%(w/v) PEG4000, 0.2 M Lithiumsulfate, 0.1 M Tris/HCL, pH 8.5; the inhibitor JRJ was introduced by extensive soaking for one week |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 6, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→35.52 Å / Num. obs: 13511 / % possible obs: 99.7 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.12 / Rsym value: 0.12 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.35→2.48 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1936 / Rsym value: 0.372 / % possible all: 98.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2pvr Resolution: 2.35→35.516 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.61 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→35.516 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 |
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