+Open data
-Basic information
Entry | Database: PDB / ID: 7ay9 | ||||||
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Title | Crystal structure of CK2 bound by compound 7 | ||||||
Components | Casein kinase II subunit alpha | ||||||
Keywords | TRANSFERASE / Inhibitor / kinase | ||||||
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: 2.25 Å | ||||||
Authors | Ferguson, A. / Collie, G.W. | ||||||
Citation | Journal: To Be Published Title: Metadynamics simulations of CK2 compound unbinding to understand slow dissociation kinetics. Authors: Date, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ay9.cif.gz | 166.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ay9.ent.gz | 130.7 KB | Display | PDB format |
PDBx/mmJSON format | 7ay9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ay9_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7ay9_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7ay9_validation.xml.gz | 29.3 KB | Display | |
Data in CIF | 7ay9_validation.cif.gz | 44.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/7ay9 ftp://data.pdbj.org/pub/pdb/validation_reports/ay/7ay9 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 40982.691 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P68400, non-specific serine/threonine protein kinase #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | 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: 3.09 Å3/Da / Density % sol: 60.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 22-26% PEG 6000 ( w/v ), 0.2 M ammonium sulfate and 0.1 M MES (pH 6.5). |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 18-ID / Wavelength: 0.97931 Å |
Detector | Type: ADSC QUANTUM 1 / Detector: CCD / Date: Apr 19, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→127.45 Å / Num. obs: 49058 / % possible obs: 99.9 % / Redundancy: 14.4 % / Biso Wilson estimate: 36.77 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 23.1 |
Reflection shell | Resolution: 2.25→2.38 Å / Redundancy: 14.5 % / Mean I/σ(I) obs: 6.7 / Num. unique obs: 7034 / CC1/2: 0.522 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: na Resolution: 2.25→18.18 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.923 / SU R Cruickshank DPI: 0.189 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.201 / SU Rfree Blow DPI: 0.169 / SU Rfree Cruickshank DPI: 0.165
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Displacement parameters | Biso max: 122.58 Å2 / Biso mean: 35.66 Å2 / Biso min: 13.46 Å2
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Refine analyze | Luzzati coordinate error obs: 0.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.25→18.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.27 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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