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Yorodumi- PDB-5m4c: Complex structure of human protein kinase CK2 catalytic subunit w... -
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-Basic information
Entry | Database: PDB / ID: 5m4c | ||||||
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Title | Complex structure of human protein kinase CK2 catalytic subunit with a thieno[2,3-d]pyrimidin inhibitor crystallized under low-salt conditions | ||||||
Components | Casein kinase II subunit alpha | ||||||
Keywords | TRANSFERASE / protein kinase CK2 / casein kinase 2 | ||||||
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: 1.935 Å | ||||||
Authors | Niefind, K. / Bischoff, N. / Yarmoluk, S.M. / Bdzhola, V.G. / Golub, A.G. / Balanda, A.O. / Prykhod'ko, A.O. | ||||||
Funding support | 1items
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Citation | Journal: Pharmaceuticals / Year: 2017 Title: Structural Hypervariability of the Two Human Protein Kinase CK2 Catalytic Subunit Paralogs Revealed by Complex Structures with a Flavonol- and a Thieno[2,3-d]pyrimidine-Based Inhibitor. Authors: Niefind, K. / Bischoff, N. / Golub, A.G. / Bdzhola, V.G. / Balanda, A.O. / Prykhod'ko, A.O. / Yarmoluk, S.M. #1: Journal: ACS Chem. Biol. / Year: 2015 Title: A Note of Caution on the Role of Halogen Bonds for Protein Kinase/Inhibitor Recognition Suggested by High- And Low-Salt CK2alpha Complex Structures. Authors: Guerra, B. / Bischoff, N. / Bdzhola, V.G. / Yarmoluk, S.M. / Issinger, O.G. / Golub, A.G. / Niefind, K. #2: Journal: Eur J Med Chem / Year: 2011 Title: Synthesis and biological evaluation of substituted (thieno[2,3-d]pyrimidin-4-ylthio)carboxylic acids as inhibitors of human protein kinase CK2. Authors: Golub, A.G. / Bdzhola, V.G. / Briukhovetska, N.V. / Balanda, A.O. / Kukharenko, O.P. / Kotey, I.M. / Ostrynska, O.V. / Yarmoluk, S.M. #3: Journal: Mol. Cell. Biochem. / Year: 2011 Title: Structure-based discovery of novel flavonol inhibitors of human protein kinase CK2. Authors: Golub, A.G. / Bdzhola, V.G. / Kyshenia, Y.V. / Sapelkin, V.M. / Prykhod'ko, A.O. / Kukharenko, O.P. / Ostrynska, O.V. / Yarmoluk, S.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5m4c.cif.gz | 160.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m4c.ent.gz | 125.8 KB | Display | PDB format |
PDBx/mmJSON format | 5m4c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5m4c_validation.pdf.gz | 763.5 KB | Display | wwPDB validaton report |
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Full document | 5m4c_full_validation.pdf.gz | 766.1 KB | Display | |
Data in XML | 5m4c_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 5m4c_validation.cif.gz | 24.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m4/5m4c ftp://data.pdbj.org/pub/pdb/validation_reports/m4/5m4c | HTTPS FTP |
-Related structure data
Related structure data | 5m44C 5m4fC 5m4iC 5m4uC 5m56C 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: Chemical | ChemComp-7EY / | ||
#3: Chemical | ChemComp-CL / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: PROTEIN STOCK SOLUTION: 6 MG/M CK2ALPHA1-335 IN 0.5 M NACL, 25 MM TRIS/HCL, PH 8.5; INHIBITOR STOCK SOLUTION: 10 MM INHIBITOR IN DMSO; PROTEIN/INHIBITOR COMPLEX SOLUTION: 90 MICROLITER ...Details: PROTEIN STOCK SOLUTION: 6 MG/M CK2ALPHA1-335 IN 0.5 M NACL, 25 MM TRIS/HCL, PH 8.5; INHIBITOR STOCK SOLUTION: 10 MM INHIBITOR IN DMSO; PROTEIN/INHIBITOR COMPLEX SOLUTION: 90 MICROLITER PROTEIN STOCK SOLUTION + 10 MICROLITER INHIBITOR STOCK SOLUTION; RESERVOIR SOLUTION: 24 % (w/v) PEG8000, 0.2 M KCl; DROP SOLUTION BEFORE EQULIBRATION: 0.3 MICROLITER PROTEIN/INHIBITOR COMPLEX SOLUTION + 0.3 MICROLITER RESERVOIR SOLUTION |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / 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: 1.935→41.6 Å / Num. obs: 23281 / % possible obs: 96 % / Redundancy: 6.3 % / Biso Wilson estimate: 21.84 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.0982 / Rsym value: 0.0982 / Net I/σ(I): 15.25 |
Reflection shell | Resolution: 1.935→2.004 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.7305 / Mean I/σ(I) obs: 2.26 / CC1/2: 0.758 / % possible all: 62 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PVR Resolution: 1.935→41.535 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.89
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.935→41.535 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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