+Open data
-Basic information
Entry | Database: PDB / ID: 6ypn | ||||||
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Title | Crystal Structure of CK2alpha with 2 molecules of ADP bound | ||||||
Components | Casein kinase II subunit alpha | ||||||
Keywords | TRANSFERASE / selective ATP competitive inhibitors | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.58 Å | ||||||
Authors | Brear, P. / Hyvonen, M. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2020 Title: Proposed Allosteric Inhibitors Bind to the ATP Site of CK2 alpha. Authors: Brear, P. / Ball, D. / Stott, K. / D'Arcy, S. / Hyvonen, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ypn.cif.gz | 91.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ypn.ent.gz | 65.8 KB | Display | PDB format |
PDBx/mmJSON format | 6ypn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ypn_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6ypn_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6ypn_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 6ypn_validation.cif.gz | 22.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yp/6ypn ftp://data.pdbj.org/pub/pdb/validation_reports/yp/6ypn | HTTPS FTP |
-Related structure data
Related structure data | 6ypgC 6yphC 6ypjC 6ypkC 5cvhS 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules B
#1: Protein | Mass: 39407.008 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Plasmid: pHAT2 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P68400, non-specific serine/threonine protein kinase |
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-Non-polymers , 5 types, 197 molecules
#2: Chemical | #3: Chemical | ChemComp-ACT / | #4: Chemical | #5: Chemical | ChemComp-PO4 / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 1.94 Å3/Da / Density % sol: 36.58 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 20 %v/v PEGSM, 10 %v/v Glycerol, 0.2 M Na Form, 0.1 M Na-Phosphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 13, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9159 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.58→53.97 Å / Num. obs: 41463 / % possible obs: 99.4 % / Redundancy: 6.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.045 / Rrim(I) all: 0.12 / Net I/σ(I): 8.1 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CVH Resolution: 1.58→53.97 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 0.007 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.111 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||
Displacement parameters | Biso max: 103.7 Å2 / Biso mean: 28.828 Å2 / Biso min: 10.95 Å2
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Refinement step | Cycle: final / Resolution: 1.58→53.97 Å
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LS refinement shell | Resolution: 1.58→1.62 Å / Rfactor Rfree error: 0
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