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- PDB-5oni: LOW-SALT STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFO... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5oni | ||||||
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Title | LOW-SALT STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA) IN COMPLEX WITH THE INDENOINDOLE-TYPE INHIBITOR 4P | ||||||
![]() | Casein kinase II subunit alpha | ||||||
![]() | TRANSFERASE / protein kinase CK2 / casein kinase 2 / indenoindole-type inhibitors | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hochscherf, J. / Lindenblatt, D. / Witulski, B. / Birus, R. / Aichele, D. / Marminon, C. / Bouaziz, Z. / Le Borgne, M. / Jose, J. / Niefind, K. | ||||||
![]() | ![]() Title: Unexpected Binding Mode of a Potent Indeno[1,2-b]indole-Type Inhibitor of Protein Kinase CK2 Revealed by Complex Structures with the Catalytic Subunit CK2 alpha and Its Paralog CK2 alpha '. Authors: Hochscherf, J. / Lindenblatt, D. / Witulski, B. / Birus, R. / Aichele, D. / Marminon, C. / Bouaziz, Z. / Le Borgne, M. / Jose, J. / Niefind, K. #1: Journal: Pharmaceuticals (Basel) / Year: 2017 Title: Development of Pharmacophore Model for Indeno[1,2-b]indoles as Human Protein Kinase CK2 Inhibitors and Database Mining. Authors: Haidar, S. / Bouaziz, Z. / Marminon, C. / Laitinen, T. / Poso, A. / Le Borgne, M. / Jose, J. #2: ![]() 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. #3: Journal: Bioorg. Med. Chem. / Year: 2012 Title: Indeno[1,2-b]indole derivatives as a novel class of potent human protein kinase CK2 inhibitors. Authors: Hundsdoerfer, C. / Hemmerling, H.J. / Goetz, C. / Totzke, F. / Bednarski, P. / Le Borgne, M. / Jose, J. #4: Journal: Biochem. Biophys. Res. Commun. / Year: 2012 Title: Novel indeno[1,2-b]indoloquinones as inhibitors of the human protein kinase CK2 with antiproliferative activity towards a broad panel of cancer cell lines. Authors: Hundsdoerfer, C. / Hemmerling, H.J. / Hamberger, J. / Le Borgne, M. / Bednarski, P. / Goetz, C. / Totzke, F. / Jose, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 304.9 KB | Display | ![]() |
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PDB format | ![]() | 248.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 28.1 KB | Display | |
Data in CIF | ![]() | 40.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5omyC ![]() 5ooiC ![]() 2pvrS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 45208.559 Da / Num. of mol.: 2 / Mutation: C-terminal deletion from Ser336 to Gln391 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P68400, non-specific serine/threonine protein kinase |
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-Non-polymers , 6 types, 313 molecules ![](data/chem/img/9YE.gif)
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![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
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![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/BU1.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-NA / | #5: Chemical | #6: Chemical | ChemComp-BU1 / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 90 MICROLITER ENZYME STOCK SOLUTION (6 MG/ML IN 500 MM NACL, 25 MM TRIS/HCL, PH 8.5) WAS MIXED WITH 10 MIKROLITER 4P STOCK SOLUTION (10 MM 4P IN DMSO). THIS MIXTURE WAS INCUBATED FOR 30 MIN ...Details: 90 MICROLITER ENZYME STOCK SOLUTION (6 MG/ML IN 500 MM NACL, 25 MM TRIS/HCL, PH 8.5) WAS MIXED WITH 10 MIKROLITER 4P STOCK SOLUTION (10 MM 4P IN DMSO). THIS MIXTURE WAS INCUBATED FOR 30 MIN AT ROOM TEMPERATURE. THE RESERVOIR SOLUTION OF THE CRYSTALLIZATION EXPERIMENT WAS 25 % (W/V) PEG5000, 0.2 M AMMONIUM SULPHATE, 0.1 M MES BUFFER, PH 6.5. PRIOR TO EQUILIBRATION THE CRYSTALLIZATION DROP WAS COMPOSED OF 1 MICROLITER RESERVOIR SOLUTION PLUS 1 MICROLITER ENZYME/4P MIXTURE., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 2→57.041 Å / Num. obs: 70221 / % possible obs: 99.51 % / Redundancy: 6.2 % / Biso Wilson estimate: 44.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06473 / Rsym value: 0.06473 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2→2.072 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.909 / Mean I/σ(I) obs: 0.93 / Num. unique obs: 6881 / CC1/2: 0.437 / Rsym value: 1.909 / % possible all: 98.84 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2PVR Resolution: 2→57.041 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 22.44
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→57.041 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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