+Open data
-Basic information
Entry | Database: PDB / ID: 7zyd | ||||||
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Title | Structure of Compound 6 Bound to CK2alpha | ||||||
Components | Casein kinase II subunit alpha | ||||||
Keywords | TRANSFERASE / Fragment based drug discovery | ||||||
Function / homology | Function and homology information regulation of chromosome separation / positive regulation of aggrephagy / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / 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 / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / 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 / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Signal transduction by L1 / peptidyl-threonine phosphorylation / Hsp90 protein binding / 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 / negative regulation of translation / regulation of cell cycle / protein stabilization / non-specific serine/threonine protein kinase / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / positive regulation of cell population proliferation / 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 / Resolution: 1.404 Å | ||||||
Authors | Brear, P. / Hyvonen, M. | ||||||
Funding support | United Kingdom, 1items
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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 | 7zyd.cif.gz | 89.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zyd.ent.gz | 65.2 KB | Display | PDB format |
PDBx/mmJSON format | 7zyd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zyd_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7zyd_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7zyd_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 7zyd_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zy/7zyd ftp://data.pdbj.org/pub/pdb/validation_reports/zy/7zyd | HTTPS FTP |
-Related structure data
Related structure data | 7zy0C 7zy2C 7zy5C 7zy8C 7zykC 7zyoC 7zyrC 8ae7C 8aecC 8aekC 8aemC 5mohS 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 (E. coli) References: UniProt: P68400, non-specific serine/threonine protein kinase | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-ATP / | #4: Chemical | ChemComp-KD6 / | #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: 2.04 Å3/Da / Density % sol: 39.63 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 112.5mM Mes pH 6.5, 35% glycerol ethoxylate, 180 mM ammonium acetate PH range: 6.5 |
-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: 0.91731 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 25, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91731 Å / Relative weight: 1 |
Reflection | Resolution: 1.404→36.23 Å / Num. obs: 61404 / % possible obs: 99.7 % / Redundancy: 3.3 % / Biso Wilson estimate: 20.43 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.024 / Rrim(I) all: 0.044 / Rsym value: 0.037 / Net I/σ(I): 16.1 / Num. measured all: 200877 |
Reflection shell | Resolution: 1.404→1.408 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 2 / Num. measured all: 54124 / Num. unique obs: 17371 / CC1/2: 0.907 / Rpim(I) all: 0.192 / Rrim(I) all: 0.346 / Rsym value: 0.446 / Net I/σ(I) obs: 3.4 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5MOH Resolution: 1.404→36.23 Å / Cor.coef. Fo:Fc: 0.9554 / Cor.coef. Fo:Fc free: 0.9494 / SU R Cruickshank DPI: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.069 / SU Rfree Blow DPI: 0.066 / SU Rfree Cruickshank DPI: 0.067
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Displacement parameters | Biso max: 108.31 Å2 / Biso mean: 26.12 Å2 / Biso min: 9.26 Å2
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Refine analyze | Luzzati coordinate error obs: 0.167 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.404→36.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.404→1.43 Å / Rfactor Rfree error: 0
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