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Yorodumi- PDB-6tew: Crystal structure of human protein kinase CK2alpha' (CSNK2A2 gene... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tew | ||||||
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Title | Crystal structure of human protein kinase CK2alpha' (CSNK2A2 gene product) in complex with the 2-aminothiazole-type inhibitor 27 | ||||||
Components | Casein kinase II subunit alpha' | ||||||
Keywords | TRANSFERASE / protein kinase CK2 / casein kinase 2 / ATP-competitive inhibitor / 2-aminothiazole derivative | ||||||
Function / homology | Function and homology information regulation of mitophagy / regulation of chromosome separation / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / positive regulation of protein targeting to mitochondrion / Receptor Mediated Mitophagy / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Maturation of hRSV A proteins ...regulation of mitophagy / regulation of chromosome separation / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / positive regulation of protein targeting to mitochondrion / Receptor Mediated Mitophagy / 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 / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / acrosomal vesicle / Signal transduction by L1 / liver regeneration / cerebral cortex development / Wnt signaling pathway / Regulation of PTEN stability and activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / KEAP1-NFE2L2 pathway / double-strand break repair / spermatogenesis / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / chromatin / nucleoplasm / ATP binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.082 Å | ||||||
Authors | Niefind, K. / Lindenblatt, D. / Jose, J. / Applegate, V.M. / Nickelsen, A. | ||||||
Funding support | Germany, 1items
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Citation | Journal: J.Med.Chem. / Year: 2020 Title: Structural and Mechanistic Basis of the Inhibitory Potency of Selected 2-Aminothiazole Compounds on Protein Kinase CK2. Authors: Lindenblatt, D. / Nickelsen, A. / Applegate, V.M. / Jose, J. / Niefind, K. #1: Journal: ACS Omega / Year: 2019 Title: Diacritic Binding of an Indenoindole Inhibitor by CK2a Paralogs Explored by a Reliable Path to Atomic Resolution CK2a' Structures. Authors: Lindenblatt, D. / Nickelsen, A. / Applegate, V.M. / Hochscherf, J. / Witulski, B. / Bouaziz, Z. / Marminon, C. / Bretner, M. / Le Borgne, M. / Jose, J. / Niefind, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tew.cif.gz | 268.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tew.ent.gz | 182.3 KB | Display | PDB format |
PDBx/mmJSON format | 6tew.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tew_validation.pdf.gz | 757.7 KB | Display | wwPDB validaton report |
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Full document | 6tew_full_validation.pdf.gz | 758.4 KB | Display | |
Data in XML | 6tew_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 6tew_validation.cif.gz | 24.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/te/6tew ftp://data.pdbj.org/pub/pdb/validation_reports/te/6tew | HTTPS FTP |
-Related 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: 42879.867 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A2, CK2A2 / Production host: Escherichia coli (E. coli) References: UniProt: P19784, non-specific serine/threonine protein kinase | ||||
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#2: Chemical | ChemComp-N5Q / | ||||
#3: Chemical | #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: 2.35 Å3/Da / Density % sol: 47.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: RESERVOIR COMPOSITION: 28 % (W/V) PEG6000, 0.9 M LICL, 0.1 M, TRIS/HCL, PH 8.5; CRYSTALLIZATION DROP COMPOSITION PRIOR TO EQUILIBRATION: 0.01 ML RESERVOIR SOLUTION PLUS 0.02 ML CK2ALPHA' ...Details: RESERVOIR COMPOSITION: 28 % (W/V) PEG6000, 0.9 M LICL, 0.1 M, TRIS/HCL, PH 8.5; CRYSTALLIZATION DROP COMPOSITION PRIOR TO EQUILIBRATION: 0.01 ML RESERVOIR SOLUTION PLUS 0.02 ML CK2ALPHA' (MUTANT CYS336SER)/INHIBITOR MB002 MIXTURE (0.180 ML 6 MG/ML CK2ALPHA-'CYS336SER, 0.5 M NACL, 25 MM TRIS/HCL, PH 8.5, MIXED AND PRE-EQUILIBRATED WITH 0.02 ML 10 MM MB002 IN DIMETHYL SULFOXIDE); the inhibitor MB002 was replaced by extensive soaking with the 2-aminothiazole-type inhibitor 27; VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9202 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9202 Å / Relative weight: 1 |
Reflection | Resolution: 1.082→46.094 Å / Num. obs: 106454 / % possible obs: 64 % / Redundancy: 6.9 % / Biso Wilson estimate: 12.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.026 / Rrim(I) all: 0.068 / Rsym value: 0.063 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.082→1.211 Å / Rmerge(I) obs: 1.585 / Num. unique obs: 5323 / CC1/2: 0.497 / Rpim(I) all: 0.654 / Rrim(I) all: 1.718 / Rsym value: 1.585 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.082→46.09 Å / SU ML: 0.0766 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.054
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.15 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.082→46.09 Å
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Refine LS restraints |
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LS refinement shell |
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