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Open data
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Basic information
Entry | Database: PDB / ID: 7zy8 | |||||||||
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Title | Crystal structure of compound 2 bound to CK2alpha | |||||||||
![]() | Casein kinase II subunit alpha | |||||||||
![]() | TRANSFERASE / Fragment based drug discovery | |||||||||
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. / Fusco, C. / Atkinson, E. / Rossmann, M. / Francis, N. / Iegre, J. / Hyvonen, M. / Spring, D. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 158.9 KB | Display | ![]() |
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PDB format | ![]() | 123.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 27.2 KB | Display | |
Data in CIF | ![]() | 40 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7zy0C ![]() 7zy2C ![]() 7zy5C ![]() 7zydC ![]() 7zykC ![]() 7zyoC ![]() 7zyrC ![]() 8ae7C ![]() 8aecC ![]() 8aekC ![]() 8aemC ![]() 5mohS S: Starting model for refinement 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
#1: Protein | Mass: 41467.793 Da / Num. of mol.: 2 Fragment: residues 2-329 and N-terminal extension GSMDIEFDDDADDDGSGSGSGSGS Mutation: R21S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P68400, non-specific serine/threonine protein kinase #2: Chemical | #3: Chemical | #4: Chemical | #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: 2.22 Å3/Da / Density % sol: 44.63 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting 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 / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 17, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96861 Å / Relative weight: 1 |
Reflection | Resolution: 1.849→166.93 Å / Num. obs: 63759 / % possible obs: 99.9 % / Redundancy: 6 % / Biso Wilson estimate: 30.91 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.049 / Rrim(I) all: 0.12 / Rsym value: 0.109 / Net I/σ(I): 13.9 / Num. measured all: 381744 / Scaling rejects: 6150 |
Reflection shell | Resolution: 1.849→1.855 Å / Redundancy: 4 % / Rmerge(I) obs: 0.808 / Mean I/σ(I) obs: 2 / Num. measured all: 44450 / Num. unique obs: 9217 / CC1/2: 0.779 / Rpim(I) all: 0.317 / Rrim(I) all: 0.708 / Rsym value: 0.808 / Net I/σ(I) obs: 2.8 / % possible all: 97.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5MOH Resolution: 1.85→166.93 Å / Cor.coef. Fo:Fc: 0.9379 / Cor.coef. Fo:Fc free: 0.9313 / SU R Cruickshank DPI: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.141 / SU Rfree Blow DPI: 0.123 / SU Rfree Cruickshank DPI: 0.123
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Displacement parameters | Biso max: 169.78 Å2 / Biso mean: 40.83 Å2 / Biso min: 9.82 Å2
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Refine analyze | Luzzati coordinate error obs: 0.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.85→166.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.9 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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