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Open data
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Basic information
Entry | Database: PDB / ID: 6l24 | ||||||
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Title | Crystal structure of CK2a1 H115Y/V116I with hematein | ||||||
![]() | Casein kinase II subunit alpha | ||||||
![]() | TRANSFERASE / protein kinase / inhibitor / complex | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Tsuyuguchi, M. / Kinoshita, T. | ||||||
![]() | ![]() Title: Structural insights for producing CK2 alpha 1-specific inhibitors. Authors: Tsuyuguchi, M. / Nakaniwa, T. / Hirasawa, A. / Nakanishi, I. / Kinoshita, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 105.1 KB | Display | ![]() |
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PDB format | ![]() | 63.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 957.9 KB | Display | ![]() |
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Full document | ![]() | 965.2 KB | Display | |
Data in XML | ![]() | 15.7 KB | Display | |
Data in CIF | ![]() | 21.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6l1zC ![]() 6l20C ![]() 6l21C ![]() 6l22C ![]() 6l23C ![]() 3warS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 40517.246 Da / Num. of mol.: 1 / Mutation: H115Y, V116I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P68400, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-E3U / ( |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.69 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: Ethylene glycol |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 18, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→43.35 Å / Num. obs: 13323 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 28.2656223859 Å2 / Rmerge(I) obs: 0.193 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.845 / Num. unique obs: 1373 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3WAR Resolution: 2.40009490218→43.3496377373 Å / SU ML: 0.311002460556 / Cross valid method: FREE R-VALUE / σ(F): 1.33789305055 / Phase error: 26.3102444413
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.5201596931 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.40009490218→43.3496377373 Å
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Refine LS restraints |
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LS refinement shell |
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