+Open data
-Basic information
Entry | Database: PDB / ID: 7a4q | ||||||
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Title | The Crystal structure of RO4613269 bound to CK2alpha | ||||||
Components | Casein kinase II subunit alpha | ||||||
Keywords | TRANSFERASE / Selective kinase 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: 1.42 Å | ||||||
Authors | Brear, P. / Hyvonen, M. | ||||||
Funding support | 1items
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Citation | Journal: Nat.Chem.Biol. / Year: 2023 Title: Chemical proteomics reveals the target landscape of 1,000 kinase inhibitors. Authors: Reinecke, M. / Brear, P. / Vornholz, L. / Berger, B.T. / Seefried, F. / Wilhelm, S. / Samaras, P. / Gyenis, L. / Litchfield, D.W. / Medard, G. / Muller, S. / Ruland, J. / Hyvonen, M. / Wilhelm, M. / Kuster, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7a4q.cif.gz | 88.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7a4q.ent.gz | 64.1 KB | Display | PDB format |
PDBx/mmJSON format | 7a4q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7a4q_validation.pdf.gz | 743.7 KB | Display | wwPDB validaton report |
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Full document | 7a4q_full_validation.pdf.gz | 747.3 KB | Display | |
Data in XML | 7a4q_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 7a4q_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/7a4q ftp://data.pdbj.org/pub/pdb/validation_reports/a4/7a4q | HTTPS FTP |
-Related structure data
Related structure data | 7zweC 7zwgC 5cvhS 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: 38944.309 Da / Num. of mol.: 1 / Mutation: K74A, K75A, K76A, R21S 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 | ChemComp-QY2 / |
#3: 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: 1.99 Å3/Da / Density % sol: 38.23 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 112.5mM Mes, 35% glycerol ethoxylate, 180 mM ammonium acetate |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Aug 7, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.42→58.81 Å / Num. obs: 58358 / % possible obs: 100 % / Redundancy: 23.7 % / Biso Wilson estimate: 18.34 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.201 / Rpim(I) all: 0.041 / Rrim(I) all: 0.205 / Net I/σ(I): 13.7 / Num. measured all: 1384264 / Scaling rejects: 1396 | ||||||||||||||||||||||||||||||
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: 1.42→49.96 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.937 / SU R Cruickshank DPI: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.07 / SU Rfree Blow DPI: 0.07 / SU Rfree Cruickshank DPI: 0.071
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Displacement parameters | Biso max: 110.55 Å2 / Biso mean: 23.84 Å2 / Biso min: 8.39 Å2
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Refinement step | Cycle: final / Resolution: 1.42→49.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.42→1.46 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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