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- PDB-7qgc: H. SAPIENS CK2 KINASE ALPHA SUBUNIT IN COMPLEX WITH THE ATP-COMPE... -
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Basic information
Entry | Database: PDB / ID: 7qgc | ||||||||||||
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Title | H. SAPIENS CK2 KINASE ALPHA SUBUNIT IN COMPLEX WITH THE ATP-COMPETITIVE INHIBITOR 5,6-DIBROMOBENZOTRIAZOLE AT PH 5.5 | ||||||||||||
![]() | Casein kinase II subunit alpha | ||||||||||||
![]() | TRANSFERASE / CK2 / CASEIN KINASE 2 / INHIBITOR / BROMO-BENZOTRIAZOLE / HALOGEN BOND / TRANSFERASE-INHIBITOR COMPLEX | ||||||||||||
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 | ![]() ![]() ![]() | ||||||||||||
![]() | Winiewska-Szajewska, M. / Czapinska, H. / Kaus-Drobek, M. / Piasecka, A. / Mieczkowska, K. / Dadlez, M. / Bochtler, M. / Poznanski, J. | ||||||||||||
Funding support | European Union, 3items
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![]() | ![]() Title: Competition between electrostatic interactions and halogen bonding in the protein-ligand system: structural and thermodynamic studies of 5,6-dibromobenzotriazole-hCK2 alpha complexes. Authors: Winiewska-Szajewska, M. / Czapinska, H. / Kaus-Drobek, M. / Fricke, A. / Mieczkowska, K. / Dadlez, M. / Bochtler, M. / Poznanski, J. #1: ![]() Title: Halogen Atoms in the Protein-Ligand System. Structural and Thermodynamic Studies of the Binding of Bromobenzotriazoles by the Catalytic Subunit of Human Protein Kinase CK2. Authors: Czapinska, H. / Winiewska-Szajewska, M. / Szymaniec-Rutkowska, A. / Piasecka, A. / Bochtler, M. / Poznanski, J. #2: Journal: Biochim Biophys Acta / Year: 2015 Title: Thermodynamics parameters for binding of halogenated benzotriazole inhibitors of human protein kinase CK2alpha. Authors: Winiewska, M. / Kucinska, K. / Makowska, M. / Poznanski, J. / Shugar, D. #3: Journal: Biochem Biophys Res Commun / Year: 2015 Title: Thermodynamic parameters for binding of some halogenated inhibitors of human protein kinase CK2. Authors: Winiewska, M. / Makowska, M. / Maj, P. / Wielechowska, M. / Bretner, M. / Poznanski, J. / Shugar, D. #4: Journal: IUBMB Life / Year: 2020 Title: A competition between hydrophobic and electrostatic interactions in protein-ligand systems. Binding of heterogeneously halogenated benzotriazoles by the catalytic subunit of human protein kinase CK2. Authors: Kasperowicz, S. / Marzec, E. / Maciejewska, A.M. / Trzybinski, D. / Bretner, M. / Wozniak, K. / Poznanski, J. / Mieczkowska, K. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 100.3 KB | Display | ![]() |
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PDB format | ![]() | 75.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 852.1 KB | Display | ![]() |
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Full document | ![]() | 853 KB | Display | |
Data in XML | ![]() | 18 KB | Display | |
Data in CIF | ![]() | 27.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7qgbC ![]() 7qgdC ![]() 7qgeC ![]() 3warS 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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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 46279.699 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-7M0 / |
#3: Chemical | ChemComp-FLC / |
#4: Chemical | ChemComp-PEG / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.05 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 20 mM sodium formate, 20 mM ammonium acetate, 20 mM sodium citrate tribasic dihydrate, 20 mM sodium potassium tartrate tetrahydrate, 20 mM sodium oxamate, 20% polyethylene glycol 550 ...Details: 20 mM sodium formate, 20 mM ammonium acetate, 20 mM sodium citrate tribasic dihydrate, 20 mM sodium potassium tartrate tetrahydrate, 20 mM sodium oxamate, 20% polyethylene glycol 550 monomethyl ester, 10% polyethylene glycol 20 000, and 0.1 M buffering solution of imidazole/MES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 3, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9117 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→45.1 Å / Num. obs: 16932 / % possible obs: 99.9 % / Redundancy: 26.26 % / Biso Wilson estimate: 39 Å2 / CC1/2: 0.995 / Rrim(I) all: 0.304 / Rsym value: 0.298 / Net I/σ(I): 10.68 |
Reflection shell | Resolution: 2.55→2.7 Å / Redundancy: 26.93 % / Mean I/σ(I) obs: 2.03 / Num. unique obs: 2658 / CC1/2: 0.8 / Rrim(I) all: 1.359 / Rsym value: 1.334 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3WAR Resolution: 2.55→45.1 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.918 / SU B: 9.531 / SU ML: 0.201 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.541 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGEN ATOMS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY THE SOLVENT MOLECULE IDENTITIES AND RELATIVE OCCUPANCIES OF STATICALLY DISORDERED RESIDUES HAVE BEEN ...Details: HYDROGEN ATOMS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY THE SOLVENT MOLECULE IDENTITIES AND RELATIVE OCCUPANCIES OF STATICALLY DISORDERED RESIDUES HAVE BEEN ASSIGNED TENTATIVELY. THERE ARE A FEW DENSITY CLUSTERS THAT MAY CORRESPOND TO SOLVENT MOLECULES BUT UNAMBIGUOUS DISTINCTION BETWEEN VARIOUS BUFFER COMPONENTS WAS NOT STRAIGHTFORWARD AND THUS THE WATER MOLECULES WERE RETAINED IN THE FINAL MODEL.
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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 max: 109.04 Å2 / Biso mean: 42.542 Å2 / Biso min: 14.09 Å2
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Refinement step | Cycle: final / Resolution: 2.55→45.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.615 Å / Rfactor Rfree error: 0
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