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- PDB-8pvo: Crystal structure of human Casein Kinase II subunit alpha (CK2a1)... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8pvo | ||||||
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Title | Crystal structure of human Casein Kinase II subunit alpha (CK2a1) in complex with allosteric compound FG5 | ||||||
![]() | Casein kinase II subunit alpha | ||||||
![]() | TRANSFERASE / Kinase / CK2 / Allosteric Inhibitor | ||||||
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 / Maturation of hRSV A proteins ...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 / Maturation of hRSV A proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / 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 proteasomal ubiquitin-dependent protein catabolic process / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Signal transduction by L1 / peptidyl-threonine phosphorylation / Hsp90 protein binding / 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 / regulation of cell cycle / non-specific serine/threonine protein kinase / negative regulation of translation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / positive regulation of cell population proliferation / apoptotic process / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kraemer, A. / Greco, F. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Funding support | 1items
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![]() | ![]() Title: Synthesis and evaluation of chemical linchpins for highly selective CK2 alpha targeting. Authors: Greco, F.A. / Kramer, A. / Wahl, L. / Elson, L. / Ehret, T.A.L. / Gerninghaus, J. / Mockel, J. / Muller, S. / Hanke, T. / Knapp, S. #1: ![]() Title: Synthesis and evaluation of chemical linchpins for highly selective CK2 alpha targeting Authors: Greco, F.A. / Kramer, A. / Wahl, L. / Elson, L. / Ehret, T.A.L. / Gerninghaus, J. / Mockel, J. / Muller, S. / Hanke, T. / Knapp, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 157.3 KB | Display | ![]() |
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PDB format | ![]() | 123 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 905.4 KB | Display | ![]() |
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Full document | ![]() | 913.9 KB | Display | |
Data in XML | ![]() | 27.8 KB | Display | |
Data in CIF | ![]() | 38.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8pvpC ![]() 8rdkC ![]() 9epvC ![]() 9epwC ![]() 9epyC ![]() 9epzC ![]() 9eq0C ![]() 9eq1C 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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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 40327.977 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 |
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-Non-polymers , 5 types, 177 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/FW3.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/FW3.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-EDO / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5.5 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 EIGER X 16M / Detector: PIXEL / Date: Mar 24, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99999 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→45.17 Å / Num. obs: 49160 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 0.999 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 2.25→2.32 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4463 / CC1/2: 0.778 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 53.18 Å2
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Refinement step | Cycle: 1 / Resolution: 2.25→45.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.308 Å / Total num. of bins used: 20
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