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Open data
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Basic information
Entry | Database: PDB / ID: 5cvf | ||||||
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Title | Crystal Structure of CK2alpha with Compound 5 bound | ||||||
![]() | Casein kinase II subunit alpha | ||||||
![]() | TRANSFERASE / CK2alpha / CK2a / fragment based drug discovery / high concentration screening / selective ATP competitive inhibitors / surface entrophy reduction | ||||||
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 | ![]() ![]() ![]() ![]() | ||||||
![]() | Brear, P. / De Fusco, C. / Georgiou, K.H. / Spring, D. / Hyvonen, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Specific inhibition of CK2 alpha from an anchor outside the active site. Authors: Brear, P. / De Fusco, C. / Hadje Georgiou, K. / Francis-Newton, N.J. / Stubbs, C.J. / Sore, H.F. / Venkitaraman, A.R. / Abell, C. / Spring, D.R. / Hyvonen, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 156.3 KB | Display | ![]() |
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PDB format | ![]() | 120.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 785.9 KB | Display | ![]() |
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Full document | ![]() | 787.6 KB | Display | |
Data in XML | ![]() | 16.4 KB | Display | |
Data in CIF | ![]() | 23.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5clpC ![]() 5cs6C ![]() 5cshC ![]() 5cspC ![]() 5csvC ![]() 5cu3C ![]() 5cu4C ![]() 5cu6C ![]() 5cvgC ![]() 5cvhC ![]() 3warS 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 39031.391 Da / Num. of mol.: 1 / Fragment: residues 2-329 / Mutation: R21S, K74A, K75A, K76A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P68400, non-specific serine/threonine protein kinase | ||
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#2: Chemical | ChemComp-54Z / | ||
#3: Chemical | ChemComp-ATP / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.93 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 112.5mM Mes pH 6.5, 35% glycerol ethoxylate, 180 mM ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 13, 2013 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.63→54.46 Å / Num. obs: 38063 / % possible obs: 97.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 22.68 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.045 / Net I/σ(I): 10.4 / Num. measured all: 123930 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3WAR Resolution: 1.63→36.08 Å / Cor.coef. Fo:Fc: 0.9303 / Cor.coef. Fo:Fc free: 0.9231 / SU R Cruickshank DPI: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.115 / SU Rfree Blow DPI: 0.097 / SU Rfree Cruickshank DPI: 0.097
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Displacement parameters | Biso max: 105.22 Å2 / Biso mean: 22.37 Å2 / Biso min: 3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.226 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.63→36.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.63→1.68 Å / Total num. of bins used: 19
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Refinement TLS params. | Method: refined / Origin x: 80.5411 Å / Origin y: 8.8188 Å / Origin z: 131.9012 Å
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Refinement TLS group | Selection details: { A|* } |