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Yorodumi- PDB-5n9n: Crystal structure of human Protein kinase CK2 catalytic subunit i... -
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-Basic information
Entry | Database: PDB / ID: 5n9n | |||||||||
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Title | Crystal structure of human Protein kinase CK2 catalytic subunit in complex with the ATP-competitive, tight-binding dibenzofuran inhibitor TF85 (4a) | |||||||||
Components | Casein kinase II subunit alpha | |||||||||
Keywords | TRANSFERASE / Protein kinase / CK2 / Casein kinase 2 / Protein phosphorylation / ATP-competitive inhititors / dibenzofuran derivatives / TIGHT-BINDING 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 / 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: 1.841 Å | |||||||||
Authors | Schnitzler, A. / Gratz, A. / Bollacke, A. / Weyrich, M. / Kucklaender, U. / Wuensch, B. / Goetz, C. / Niefind, K. / Jose, J. | |||||||||
Citation | Journal: Pharmaceuticals / Year: 2018 Title: A pi-Halogen Bond of Dibenzofuranones with the Gatekeeper Phe113 in Human Protein Kinase CK2 Leads to Potent Tight Binding Inhibitors. Authors: Schnitzler, A. / Gratz, A. / Bollacke, A. / Weyrich, M. / Kucklander, U. / Wunsch, B. / Gotz, C. / Niefind, K. / Jose, J. #1: 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. #2: Journal: J. Mol. Biol. / Year: 2005 Title: Inclining the purine base binding plane in protein kinase CK2 by exchanging the flanking side-chains generates a preference for ATP as a cosubstrate. Authors: Yde, C.W. / Ermakova, I. / Issinger, O.G. / Niefind, K. #3: Journal: Pharmaceuticals (Basel) / 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. #4: Journal: Biochim. Biophys. Acta / Year: 2012 Title: TF--a novel cell-permeable and selective inhibitor of human protein kinase CK2 induces apoptosis in the prostate cancer cell line LNCaP. Authors: Goetz, C. / Gratz, A. / Kucklaender, U. / Jose, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5n9n.cif.gz | 161.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n9n.ent.gz | 127.2 KB | Display | PDB format |
PDBx/mmJSON format | 5n9n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5n9n_validation.pdf.gz | 716.1 KB | Display | wwPDB validaton report |
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Full document | 5n9n_full_validation.pdf.gz | 719.2 KB | Display | |
Data in XML | 5n9n_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 5n9n_validation.cif.gz | 23 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n9/5n9n ftp://data.pdbj.org/pub/pdb/validation_reports/n9/5n9n | HTTPS FTP |
-Related structure data
Related structure data | 5n9kC 5n9lC 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 / Fragment: UNP residues 1-335 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-KC5 / ( | ||||
#3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-GOL / #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: 1.93 Å3/Da / Density % sol: 36.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: Prior to the crystallization the Inhibitor TF85 was solubilized in 100 % DMSO in a concentration of 10 mM. This TF85 stock solution was mixed with human CK2alpha (construct 1-335; Protein ...Details: Prior to the crystallization the Inhibitor TF85 was solubilized in 100 % DMSO in a concentration of 10 mM. This TF85 stock solution was mixed with human CK2alpha (construct 1-335; Protein concentration 8-10 mg/ml in 500 mM sodium chloride, 25 mM Tris/HCl pH 8.5) in a ratio of 1:10. After a short time of incubation, this mixture was mixed with reservoir solution [32 % (w/v) PEG4000, 0.2 M ammonium acetate, 0.1 M citrate pH 5.6] in a ratio of 5:2. 3.5 microliter of these mixtures were then equilibrated against the reservoir solution. The crystal growth was induced by seeding with 150 nanoliter seeding suspension after an equilibration time of two days. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99987 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 12, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99987 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→45.51 Å / Num. obs: 25795 / % possible obs: 96.4 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.84→1.88 Å / Redundancy: 3 % / Rmerge(I) obs: 0.75 / Num. unique obs: 1395 / CC1/2: 0.644 / Rsym value: 0.75 / % possible all: 84.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2pvr Resolution: 1.841→34.165 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.35
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.841→34.165 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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