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Yorodumi- PDB-7a4b: Crystal structure of human protein kinase CK2alpha (CSNK2A1 gene ... -
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-Basic information
Entry | Database: PDB / ID: 7a4b | ||||||
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Title | Crystal structure of human protein kinase CK2alpha (CSNK2A1 gene product) in complex with the ATP-competitive inhibitor 5,6-dibromo-1H-triazolo[4,5-b]pyridine | ||||||
Components | Casein kinase II subunit alpha | ||||||
Keywords | TRANSFERASE / protein kinase CK2 / casein kinase 2 / ATP-competitive inhibitor | ||||||
Function / homology | Function and homology information regulation of chromosome separation / positive regulation of aggrephagy / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Sin3-type complex / Maturation of hRSV A proteins ...regulation of chromosome separation / positive regulation of aggrephagy / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Sin3-type complex / Maturation of hRSV A proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / 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 proteasomal ubiquitin-dependent protein catabolic process / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Signal transduction by L1 / peptidyl-threonine phosphorylation / Hsp90 protein binding / 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 / negative regulation of translation / regulation of cell cycle / protein stabilization / non-specific serine/threonine protein kinase / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / positive regulation of cell population proliferation / apoptotic process / 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: 2.06 Å | ||||||
Authors | Niefind, K. / Lindenblatt, D. / Toelzer, C. / Bretner, M. / Chojnacki, K. / Wielechowska, M. / Winska, P. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Bioorg.Chem. / Year: 2021 Title: Synthesis, biological properties and structural study of new halogenated azolo[4,5-b]pyridines as inhibitors of CK2 kinase. Authors: Chojnacki, K. / Lindenblatt, D. / Winska, P. / Wielechowska, M. / Toelzer, C. / Niefind, K. / Bretner, M. #1: Journal: Bioorg. Chem. / Year: 2018 Title: Biological properties and structural study of new aminoalkyl derivatives of benzimidazole and benzotriazole, dual inhibitors of CK2 and PIM1 kinases. Authors: Chojnacki, K. / Winska, P. / Wielechowska, M. / Lukowska-Chojnacka, E. / Toelzer, C. / Niefind, K. / Bretner, M. #2: Journal: ACS Omega / Year: 2019 Title: Diacritic Binding of an Indenoindole Inhibitor by CK2alpha Paralogs Explored by a Reliable Path to Atomic Resolution CK2alpha' 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. #3: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7a4b.cif.gz | 361.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7a4b.ent.gz | 247.3 KB | Display | PDB format |
PDBx/mmJSON format | 7a4b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7a4b_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7a4b_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7a4b_validation.xml.gz | 28.7 KB | Display | |
Data in CIF | 7a4b_validation.cif.gz | 40.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/7a4b ftp://data.pdbj.org/pub/pdb/validation_reports/a4/7a4b | HTTPS FTP |
-Related structure data
Related structure data | 7a1bC 7a1zC 7a22C 7a2hC 7a49C 7a4cC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: givenMatrix: (0.0100894481208, -0.995769123504, 0.0913348548625), (0.999920155022, 0.00935200542842, -0.00849844543709), (0.00760832550556, 0.0914133068573, 0.995783972914)Vector: - ...NCS oper: (Code: given Matrix: (0.0100894481208, -0.995769123504, 0.0913348548625), Vector: |
-Components
#1: Protein | Mass: 40066.742 Da / Num. of mol.: 2 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: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 3.18 Å3/Da / Density % sol: 61.3 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 1 MIKROLITER OF THE CK2ALPHA/INHIBITOR MIXTURE (COMPOSITION: 7 MG/ML CK2ALPHA ENZYME, 1 MILLIMOLAR INHIBITOR, 10 % DIMETHYL SULFOXIDE, 450 MM NACL, 22.5 MM TRIS/HCL, PH 8.5) WAS MIXED WITH 1 ...Details: 1 MIKROLITER OF THE CK2ALPHA/INHIBITOR MIXTURE (COMPOSITION: 7 MG/ML CK2ALPHA ENZYME, 1 MILLIMOLAR INHIBITOR, 10 % DIMETHYL SULFOXIDE, 450 MM NACL, 22.5 MM TRIS/HCL, PH 8.5) WAS MIXED WITH 1 MIKROLITER RESERVOIR SOLUTION (COMPOSITION: 25 % PEG3350, 0.2 M AMMONIUM SULPHATE, 0.1 M BIS-TRIS BUFFER, PH 5.5) FOLLOWED BY VAPOUR DIFFUSION EQUILIBRATION AGAINST THE RESERVOIR SOLUTION. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976251 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 13, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976251 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→90.035 Å / Num. obs: 46838 / % possible obs: 73.3 % / Redundancy: 25.7 % / Biso Wilson estimate: 33.21 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.178 / Rpim(I) all: 0.036 / Rrim(I) all: 0.181 / Rsym value: 0.178 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2.06→2.26 Å / Redundancy: 18.1 % / Rmerge(I) obs: 2.105 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2341 / CC1/2: 0.483 / Rpim(I) all: 0.492 / Rrim(I) all: 2.166 / Rsym value: 2.105 / % possible all: 15.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PVR Resolution: 2.06→90.035 Å / SU ML: 0.1917 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.3157 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.63 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.06→90.035 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.560662666119 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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