+Open data
-Basic information
Entry | Database: PDB / ID: 8aek | |||||||||
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Title | Structure of Compound 14 bound to CK2alpha | |||||||||
Components | Casein kinase II subunit alpha | |||||||||
Keywords | TRANSFERASE / Fragment Based | |||||||||
Function / homology | Function and homology information 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 / Synthesis of PC / Sin3-type complex / 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 / Synthesis of PC / Sin3-type complex / 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 / Signal transduction by L1 / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / peptidyl-threonine phosphorylation / Hsp90 protein binding / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / positive regulation of protein catabolic process / rhythmic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / KEAP1-NFE2L2 pathway / double-strand break repair / kinase activity / peptidyl-serine phosphorylation / positive regulation of cell growth / 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 / positive regulation of cell population proliferation / DNA damage response / apoptotic process / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | |||||||||
Authors | Brear, P. / Fusco, C. / Atkinson, E. / Iegre, J. / Francis-Newton, N. / Venkotaraman, A. / Spring, D. / Hyvonen, M. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Rsc Med Chem / Year: 2022 Title: A fragment-based approach leading to the discovery of inhibitors of CK2 alpha with a novel mechanism of action. Authors: Brear, P. / De Fusco, C. / Atkinson, E.L. / Iegre, J. / Francis-Newton, N.J. / Venkitaraman, A.R. / Hyvonen, M. / Spring, D.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8aek.cif.gz | 92.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8aek.ent.gz | 67.2 KB | Display | PDB format |
PDBx/mmJSON format | 8aek.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8aek_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8aek_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8aek_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 8aek_validation.cif.gz | 24.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/8aek ftp://data.pdbj.org/pub/pdb/validation_reports/ae/8aek | HTTPS FTP |
-Related structure data
Related structure data | 7zy0C 7zy2C 7zy5C 7zy8C 7zydC 7zykC 7zyoC 7zyrC 8ae7C 8aecC 8aemC 5cvhS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 39031.391 Da / Num. of mol.: 1 / Mutation: R21S, K74A, K75A, K76A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P68400, non-specific serine/threonine protein kinase | ||||
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#2: Chemical | ChemComp-LVL / | ||||
#3: Chemical | ChemComp-ATP / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 112.5mM Mes pH 6.5, 35% glycerol ethoxylate, 180 mM ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: BRUKER IMUS 3.0 MICROFOCUS / Wavelength: 1.54 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Sep 21, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→100 Å / Num. obs: 37717 / % possible obs: 99.5 % / Redundancy: 9.64 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.0613 / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 1.65→1.75 Å / Redundancy: 3.38 % / Rmerge(I) obs: 0.3099 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 6090 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CVH Resolution: 1.65→36.13 Å / Cor.coef. Fo:Fc: 0.9551 / Cor.coef. Fo:Fc free: 0.9421 / SU R Cruickshank DPI: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.102 / SU Rfree Blow DPI: 0.095 / SU Rfree Cruickshank DPI: 0.094
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Displacement parameters | Biso max: 92.8 Å2 / Biso mean: 17.98 Å2 / Biso min: 4.4 Å2
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Refine analyze | Luzzati coordinate error obs: 0.168 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.65→36.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.7 Å / Rfactor Rfree error: 0 / Total num. of bins used: 19
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