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Open data
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Basic information
Entry | Database: PDB / ID: 6z83 | ||||||
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Title | CK2 alpha bound to chemical probe SGC-CK2-1 | ||||||
![]() | Casein kinase II subunit alpha | ||||||
![]() | TRANSFERASE / Kinase / Chemical Probe / Inhibitor / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Kraemer, A. / Wells, C. / Drewry, D.H. / Pickett, J.E. / Axtman, A.D. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Development of a potent and selective chemical probe for the pleiotropic kinase CK2. Authors: Wells, C.I. / Drewry, D.H. / Pickett, J.E. / Tjaden, A. / Kramer, A. / Muller, S. / Gyenis, L. / Menyhart, D. / Litchfield, D.W. / Knapp, S. / Axtman, A.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 163.9 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1016.4 KB | Display | ![]() |
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Full document | ![]() | 1019.7 KB | Display | |
Data in XML | ![]() | 28.1 KB | Display | |
Data in CIF | ![]() | 40.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6z84C ![]() 6yulS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 42799.633 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P68400, non-specific serine/threonine protein kinase #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-PEG / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 58.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M ammonia sulphate 0.1 M bis-tris pH 5.5 23-26% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 15, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99999 Å / Relative weight: 1 |
Reflection | Resolution: 2.17→44.89 Å / Num. obs: 54337 / % possible obs: 100 % / Redundancy: 26.5 % / CC1/2: 0.999 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2.17→2.23 Å / Num. unique obs: 4362 / CC1/2: 0.761 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6yul Resolution: 2.171→44.89 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.932 / SU B: 6.166 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / ESU R: 0.217 / ESU R Free: 0.183 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.336 Å2
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Refinement step | Cycle: LAST / Resolution: 2.171→44.89 Å
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Refine LS restraints |
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LS refinement shell |
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