[English] 日本語
![](img/lk-miru.gif)
- PDB-7a1z: Crystal structure of human protein kinase CK2alpha' (CSNK2A2 gene... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7a1z | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human protein kinase CK2alpha' (CSNK2A2 gene product) in complex with the ATP-competitive inhibitor 6-bromo-5-chloro-1H-triazolo[4,5-b]pyridine | ||||||
![]() | Casein kinase II subunit alpha' | ||||||
![]() | TRANSFERASE / protein kinase CK2 / casein kinase 2 / ATP-competitive inhibitor | ||||||
Function / homology | ![]() 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 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 / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / cell cycle / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / chromatin / nucleoplasm / ATP binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Niefind, K. / Lindenblatt, D. / Toelzer, C. / Bretner, M. / Chojnacki, K. / Wielechowska, M. / Winska, P. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() 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: ![]() 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: ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 280.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 190.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 748.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 749.6 KB | Display | |
Data in XML | ![]() | 18 KB | Display | |
Data in CIF | ![]() | 27.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7a1bC ![]() 7a22C ![]() 7a2hC ![]() 7a49C ![]() 7a4bC ![]() 7a4cC C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 42879.867 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P19784, non-specific serine/threonine protein kinase | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-QWN / | ||||
#3: Chemical | ChemComp-CL / | ||||
#4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.06 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Reservoir composition: 28 % (w/v) PEG6000, 0.9 M LiCl, 0.1 M, Tris/HCl, pH 8.5; drop composition prior to equilibration: 0.01 ml reservoir solution + 0.02 ml CK2alpha' (mutant Cys336Ser) ...Details: Reservoir composition: 28 % (w/v) PEG6000, 0.9 M LiCl, 0.1 M, Tris/HCl, pH 8.5; drop composition prior to equilibration: 0.01 ml reservoir solution + 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 initial inhibitor MB002 was replaced by the inhibitor 6-bromo-5-chloro-1H-triazolo[4,5-b]pyridine by extensive crystal soaking. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 14, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87313 Å / Relative weight: 1 |
Reflection | Resolution: 1.024→46.434 Å / Num. obs: 155664 / % possible obs: 77.7 % / Redundancy: 9 % / Biso Wilson estimate: 10.52 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.03 / Rrim(I) all: 0.093 / Rsym value: 0.088 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.024→1.086 Å / Rmerge(I) obs: 1.38 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 7786 / CC1/2: 0.5 / Rpim(I) all: 0.596 / Rrim(I) all: 1.513 / Rsym value: 1.38 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.024→46.43 Å / SU ML: 0.0778 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 17.8544 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.21 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.024→46.43 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|