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Yorodumi- PDB-4ib5: Structure of human protein kinase CK2 catalytic subunit in comple... -
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-Basic information
Entry | Database: PDB / ID: 4ib5 | ||||||
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Title | Structure of human protein kinase CK2 catalytic subunit in complex with a CK2beta-competitive cyclic peptide | ||||||
Components |
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Keywords | TRANSFERASE / protein kinase fold / protein phosphorylation / Binding of CK2beta / Phosphorylation / Nucleus | ||||||
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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Raaf, J. / Guerra, B. / Neundorf, I. / Bopp, B. / Issinger, O.-G. / Jose, J. / Pietsch, M. / Niefind, K. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2013 Title: First structure of protein kinase CK2 catalytic subunit with an effective CK2 beta-competitive ligand Authors: Raaf, J. / Guerra, B. / Neundorf, I. / Bopp, B. / Issinger, O.G. / Jose, J. / Pietsch, M. / Niefind, K. #1: Journal: Embo J. / Year: 2001 Title: Crystal structure of human protein kinase CK2: insights into basic properties of the CK2 holoenzyme Authors: Niefind, K. / Guerra, B. / Ermakowa, I. / Issinger, O.G. #2: Journal: Biochem.J. / Year: 2007 Title: Structure-based design of small peptide inhibitors of protein kinase CK2 subunit interaction. Authors: Laudet, B. / Barette, C. / Dulery, V. / Renaudet, O. / Dumy, P. / Metz, A. / Prudent, R. / Deshiere, A. / Dideberg, O. / Filhol, O. / Cochet, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ib5.cif.gz | 462.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ib5.ent.gz | 398.7 KB | Display | PDB format |
PDBx/mmJSON format | 4ib5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ib5_validation.pdf.gz | 485.5 KB | Display | wwPDB validaton report |
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Full document | 4ib5_full_validation.pdf.gz | 498.8 KB | Display | |
Data in XML | 4ib5_validation.xml.gz | 43.8 KB | Display | |
Data in CIF | 4ib5_validation.cif.gz | 61.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ib/4ib5 ftp://data.pdbj.org/pub/pdb/validation_reports/ib/4ib5 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 40066.742 Da / Num. of mol.: 3 / Fragment: UNP residues 1-355 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 #2: Protein/peptide | Mass: 1413.692 Da / Num. of mol.: 4 / Source method: obtained synthetically Details: The molecule was synthesized by solid-phase peptide synthesis. #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 2.46 Å3/Da / Density % sol: 50.1 % |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
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Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→45.693 Å / Num. obs: 63979 / % possible obs: 99.6 % / Biso Wilson estimate: 39.1 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→45.693 Å / Occupancy max: 1 / Occupancy min: 0.38 / SU ML: 0.21 / σ(F): 0 / Phase error: 21.5 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 187.36 Å2 / Biso mean: 66.8099 Å2 / Biso min: 23.01 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→45.693 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23
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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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