+Open data
-Basic information
Entry | Database: PDB / ID: 5cvh | |||||||||
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Title | Crystal Structure of CK2alpha | |||||||||
Components | Casein kinase II subunit alphaCasein kinase 2 | |||||||||
Keywords | TRANSFERASE / CK2alpha / CK2a / fragment based drug discovery / high concentration screening / selective ATP competitive inhibitors / surface entrophy reduction | |||||||||
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 / 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 / negative regulation of apoptotic signaling pathway / positive regulation of Wnt signaling pathway / chaperone-mediated protein folding / negative regulation of ubiquitin-dependent protein catabolic process / Signal transduction by L1 / Hsp90 protein binding / peptidyl-threonine phosphorylation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / positive regulation of protein catabolic process / rhythmic process / KEAP1-NFE2L2 pathway / double-strand break repair / kinase activity / positive regulation of cell growth / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / negative regulation of translation / protein stabilization / regulation of cell cycle / non-specific serine/threonine protein kinase / 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 | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.848 Å | |||||||||
Authors | Brear, P. / De Fusco, C. / Georgiou, K.H. / Spring, D. / Hyvonen, M. | |||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Chem Sci / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cvh.cif.gz | 300 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cvh.ent.gz | 244.3 KB | Display | PDB format |
PDBx/mmJSON format | 5cvh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cv/5cvh ftp://data.pdbj.org/pub/pdb/validation_reports/cv/5cvh | HTTPS FTP |
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-Related structure data
Related structure data | 5clpC 5cs6C 5cshC 5cspC 5csvC 5cu3C 5cu4C 5cu6C 5cvfC 5cvgC 3warS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: 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.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Plasmid: pHAT4 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P68400, non-specific serine/threonine protein kinase |
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-Non-polymers , 5 types, 227 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-ACT / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.7 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 107mM Mes pH 6.5, 29% glycerol ethoxylate, 1 M ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9188 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 28, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9188 Å / Relative weight: 1 |
Reflection | Resolution: 1.848→166.55 Å / Num. obs: 64008 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 38.54 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 1.848→1.855 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.852 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.852 / Rejects: 0 / % possible all: 99.5 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WAR Resolution: 1.848→166.55 Å / Cor.coef. Fo:Fc: 0.9447 / Cor.coef. Fo:Fc free: 0.9373 / SU R Cruickshank DPI: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.141 / SU Rfree Blow DPI: 0.121 / SU Rfree Cruickshank DPI: 0.122
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Displacement parameters | Biso max: 214.01 Å2 / Biso mean: 61.23 Å2 / Biso min: 19.48 Å2
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Refine analyze | Luzzati coordinate error obs: 0.322 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.848→166.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.848→1.89 Å
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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