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Yorodumi- PDB-5ts8: Z. MAYS CK2 KINASE ALPHA SUBUNIT IN COMPLEX WITH THE ATP-COMPETIT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ts8 | |||||||||
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Title | Z. MAYS CK2 KINASE ALPHA SUBUNIT IN COMPLEX WITH THE ATP-COMPETITIVE INHIBITOR 5,6-DIBROMOBENZOTRIAZOLE | |||||||||
Components | Protein kinase CK2 catalytic subunit CK2 alpha-3 | |||||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / CK2 / CASEIN KINASE 2 / INHIBITOR / BROMO-BENZOTRIAZOLE / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX / HALOGEN BOND | |||||||||
Function / homology | Function and homology information protein kinase CK2 complex / regulation of cell cycle / non-specific serine/threonine protein kinase / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Zea mays (maize) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | |||||||||
Authors | Winiewska, M. / Kucinska, K. / Czapinska, H. / Piasecka, A. / Bochtler, M. / Poznanski, J. | |||||||||
Funding support | Poland, 2items
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Citation | Journal: To Be Published Title: STRUCTURAL AND THERMODYNAMIC ANALYSIS OF 5,6-DIBROMOBENZOTRIAZOLE BINDING TO CASEIN KINASE 2 ALPHA Authors: Winiewska, M. / Kucinska, K. / Czapinska, H. / Piasecka, A. / Bochtler, M. / Poznanski, J. #1: 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. #2: 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. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ts8.cif.gz | 182.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ts8.ent.gz | 144.1 KB | Display | PDB format |
PDBx/mmJSON format | 5ts8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ts/5ts8 ftp://data.pdbj.org/pub/pdb/validation_reports/ts/5ts8 | HTTPS FTP |
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-Related structure data
Related structure data | 4rlkS S: Starting model for refinement |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 40436.230 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zea mays (maize) / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9FQF5, UniProt: P28523*PLUS |
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-Non-polymers , 9 types, 463 molecules
#2: Chemical | ChemComp-7M0 / | ||||||||||||||
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#3: Chemical | #4: Chemical | ChemComp-FMT / | #5: Chemical | ChemComp-DMS / | #6: Chemical | ChemComp-ACT / | #7: Chemical | #8: Chemical | ChemComp-BME / | #9: Chemical | ChemComp-GOL / | #10: Water | ChemComp-HOH / | |
-Details
Compound details | THE ACTIVE FORM OF THE PROTEIN KINASE CK2 IS HETEROTETRAMERIC AND COMPOSED OF TWO ALPHA SUBUNITS ...THE ACTIVE FORM OF THE PROTEIN KINASE CK2 IS HETEROTETR |
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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: 2.19 Å3/Da / Density % sol: 43.82 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: pH 7.5 (1M Sodium HEPES; MOPS), 40% v/v PEG 500* MME; 20 % w/v PEG 20K; 0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Sodium potassium tartrate ...Details: pH 7.5 (1M Sodium HEPES; MOPS), 40% v/v PEG 500* MME; 20 % w/v PEG 20K; 0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Sodium potassium tartrate tetrahydrate; 0.2M Sodium oxamate PH range: 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9116 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 6, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9116 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→51.96 Å / Num. obs: 60461 / % possible obs: 98 % / Redundancy: 3.23 % / Biso Wilson estimate: 22.5 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.057 / Rsym value: 0.048 / Net I/σ(I): 14.19 |
Reflection shell | Resolution: 1.45→1.54 Å / Redundancy: 2.78 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.81 / CC1/2: 0.84 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4RLK Resolution: 1.45→51.96 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.971 / SU B: 2.551 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.065 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TLS HAS BEEN USED AND U VALUES GENERATED WITH TLS CONTRIBUTION ADDED. DIFFERENCE DENSITY NEXT TO THE OH OXYGEN ATOM OF TYR257 AND TYR26 ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TLS HAS BEEN USED AND U VALUES GENERATED WITH TLS CONTRIBUTION ADDED. DIFFERENCE DENSITY NEXT TO THE OH OXYGEN ATOM OF TYR257 AND TYR26 MIGHT INDICATE THE X-RAY RADIATION INDUCED HYDROPEROXIDE FORMATION. THE COMPLICATED COMPOSITION OF THE CRYSTALLIZATION BUFFER PRECLUDED UNAMBIGUOUS IDENTIFICATION OF THE LIGANDS. IN SOME CASES MIXTURES OF DIFFERENT COMPOUNDS ARE POSSIBLE EG TARTRATE, OXAMATE, ACETATE (AND DMSO), IN OTHER CASES THE LIGAND IDENTITY COULD NOT BE GUESSED AND THE DIFFERENCE DENSITY COULD AT BEST BE MODELLED AS A SET OF DISORDERED WATER MOLECULES.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.744 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→51.96 Å
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Refine LS restraints |
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