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Yorodumi- PDB-6spx: Structure of protein kinase CK2 catalytic subunit in complex with... -
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-Basic information
Entry | Database: PDB / ID: 6spx | ||||||
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Title | Structure of protein kinase CK2 catalytic subunit in complex with the CK2beta-competitive bisubstrate inhibitor ARC1502 | ||||||
Components |
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Keywords | TRANSFERASE / protein kinase CK2 casein kinase 2 bisubstrate inhibitor | ||||||
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 / Maturation of hRSV A proteins / 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 ubiquitin-dependent protein catabolic process / Signal transduction by L1 / peptidyl-threonine phosphorylation / Hsp90 protein binding / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / 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 / protein stabilization / negative regulation of translation / non-specific serine/threonine protein kinase / regulation of cell cycle / 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) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.994 Å | ||||||
Authors | Niefind, K. / Schnitzler, A. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Bioorg.Chem. / Year: 2020 Title: Unexpected CK2 beta-antagonistic functionality of bisubstrate inhibitors targeting protein kinase CK2. Authors: Pietsch, M. / Viht, K. / Schnitzler, A. / Ekambaram, R. / Steinkruger, M. / Enkvist, E. / Nienberg, C. / Nickelsen, A. / Lauwers, M. / Jose, J. / Uri, A. / Niefind, K. #1: Journal: Org. Biomol. Chem. / Year: 2012 Title: A subnanomolar fluorescent probe for protein kinase CK2 interaction studies. Authors: Enkvist, E. / Viht, K. / Bischoff, N. / Vahter, J. / Saaver, S. / Raidaru, G. / Issinger, O.G. / Niefind, K. / Uri, A. #2: Journal: J. Mol. Biol. / Year: 2003 Title: Crystal structure of a C-terminal deletion mutant of human protein kinase CK2 catalytic subunit. Authors: Ermakova, I. / Boldyreff, B. / Issinger, O.G. / Niefind, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6spx.cif.gz | 158.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6spx.ent.gz | 124.3 KB | Display | PDB format |
PDBx/mmJSON format | 6spx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6spx_validation.pdf.gz | 761.4 KB | Display | wwPDB validaton report |
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Full document | 6spx_full_validation.pdf.gz | 763.1 KB | Display | |
Data in XML | 6spx_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 6spx_validation.cif.gz | 22 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sp/6spx ftp://data.pdbj.org/pub/pdb/validation_reports/sp/6spx | HTTPS FTP |
-Related structure data
Related structure data | 6spwC 2pvrS C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 40066.742 Da / Num. of mol.: 1 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: Protein/peptide | Mass: 837.722 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Chemical | ChemComp-9AB / |
#4: 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: 38.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1 microliter of the CK2alpha/ARC1502 mixture (composition: 7 mg/ml CK2alpha enzyme, 1 mM ARC1502, 10 % dimethyl sulfoxide, 450 mM NaCl, 25 mM Tris/HCl, pH 8.5) was mixed with 2.5 mikroliter ...Details: 1 microliter of the CK2alpha/ARC1502 mixture (composition: 7 mg/ml CK2alpha enzyme, 1 mM ARC1502, 10 % dimethyl sulfoxide, 450 mM NaCl, 25 mM Tris/HCl, pH 8.5) was mixed with 2.5 mikroliter reservoir solution (composition: 30 % PEG4000, 0.2 M ammonium acetate, 0.1 M sodium citrate, pH 5.6) followed by vapour diffusion equilibration against 100 microliter of the reservoir solution. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 20, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.994→49.723 Å / Num. obs: 19533 / % possible obs: 93.38 % / Redundancy: 4.4 % / Biso Wilson estimate: 28.54 Å2 / CC1/2: 0.967 / Rmerge(I) obs: 0.2085 / Rsym value: 0.2085 / Net I/σ(I): 15.91 |
Reflection shell | Resolution: 1.994→2.266 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.5205 / Mean I/σ(I) obs: 2.76 / Num. unique obs: 3380 / CC1/2: 0.669 / Rsym value: 0.5205 / % possible all: 66.25 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PVR Resolution: 1.994→49.72 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.71
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.994→49.72 Å
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Refine LS restraints |
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LS refinement shell |
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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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