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- PDB-3kxg: Crystal structure of Z. mays CK2 kinase alpha subunit in complex ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3kxg | ||||||
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Title | Crystal structure of Z. mays CK2 kinase alpha subunit in complex with the inhibitor 3,4,5,6,7-pentabromo-1H-indazole (K64) | ||||||
![]() | Casein kinase II subunit alpha | ||||||
![]() | Transferase/Transferase inhibitor / Protein kinase CK2-inhibitor complex / ATP-binding / Kinase / Nucleotide-binding / Serine/threonine-protein kinase / Transferase / Transferase-Transferase inhibitor complex | ||||||
Function / homology | ![]() regulation of transcription by RNA polymerase I / regulation of transcription by RNA polymerase III / protein kinase CK2 complex / non-specific serine/threonine protein kinase / regulation of cell cycle / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / ATP binding ...regulation of transcription by RNA polymerase I / regulation of transcription by RNA polymerase III / protein kinase CK2 complex / non-specific serine/threonine protein kinase / regulation of cell cycle / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / ATP binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Papinutto, E. / Franchin, C. / Battistutta, R. | ||||||
![]() | ![]() Title: ATP site-directed inhibitors of protein kinase CK2: an update. Authors: Sarno, S. / Papinutto, E. / Franchin, C. / Bain, J. / Elliott, M. / Meggio, F. / Kazimierczuk, Z. / Orzeszko, A. / Zanotti, G. / Battistutta, R. / Pinna, L.A. #1: ![]() Title: Inspecting the structure-activity relationship of protein kinase CK2 inhibitors derived from tetrabromo-benzimidazole. Authors: Battistutta, R. / Mazzorana, M. / Sarno, S. / Kazimierczuk, Z. / Zanotti, G. / Pinna, L.A. #2: ![]() Title: The ATP-binding site of protein kinase CK2 holds a positive electrostatic area and conserved water molecules. Authors: Battistutta, R. / Mazzorana, M. / Cendron, L. / Bortolato, A. / Sarno, S. / Kazimierczuk, Z. / Zanotti, G. / Moro, S. / Pinna, L.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 83.2 KB | Display | ![]() |
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PDB format | ![]() | 65.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1020 KB | Display | ![]() |
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Full document | ![]() | 1023.9 KB | Display | |
Data in XML | ![]() | 17.1 KB | Display | |
Data in CIF | ![]() | 25.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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 on special symmetry positions |
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Components
#1: Protein | Mass: 38689.395 Da / Num. of mol.: 1 / Fragment: ALPHA SUBUNIT Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P28523, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-K6X / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 20% PEG 4000, 0.2M Na-acetate, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 6, 2008 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972991 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→69.34 Å / Num. all: 41479 / Num. obs: 41272 / % possible obs: 99.5 % / Redundancy: 4 % / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 4 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.441 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: Rigid body in an isomorphous cell Resolution: 1.7→69.34 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.928 / SU B: 6.099 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.126 / 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: 19.519 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→69.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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