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- PDB-6hmc: STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALP... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6hmc | ||||||
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Title | STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA'; CSNK2A2 gene product) IN COMPLEX WITH THE INDENOINDOLE-TYPE INHIBITOR THN27 | ||||||
![]() | Casein kinase II subunit alpha' | ||||||
![]() | TRANSFERASE / protein kinase CK2 / casein kinase 2 / catalytic subunit CK2alpha' / CSNK2A2 | ||||||
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 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Niefind, K. / Lindenblatt, D. / Dimper, V. / Jose, J. / Le Borgne, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Diacritic Binding of an Indenoindole Inhibitor by CK2 alpha Paralogs Explored by a Reliable Path to Atomic Resolution CK2 alpha ' 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. #1: ![]() 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 CK2alpha and Its Paralog CK2alpha' Authors: Hochscherf, J. / Lindenblatt, D. / Witulski, B. / Birus, R. / Aichele, D. / Marminon, C. / Bouaziz, Z. / Le Borgne, M. / Jose, J. / Niefind, K. #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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 241.7 KB | Display | ![]() |
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PDB format | ![]() | 196.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 805.6 KB | Display | ![]() |
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Full document | ![]() | 807.9 KB | Display | |
Data in XML | ![]() | 19.1 KB | Display | |
Data in CIF | ![]() | 29.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 42879.867 Da / Num. of mol.: 1 / Mutation: C336S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P19784, non-specific serine/threonine protein kinase | ||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-FXB / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.91 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 180 MICROLITER ENZYME STOCK SOLUTION (6 MG/ML IN 500 MM NACL, 25 MM TRIS/HCL, PH 8.5) WERE MIXED and incubated WITH 20 MIKROLITER of a STOCK SOLUTION of the inhibitor 4B0 (10 MM 4B0 IN DMSO). ...Details: 180 MICROLITER ENZYME STOCK SOLUTION (6 MG/ML IN 500 MM NACL, 25 MM TRIS/HCL, PH 8.5) WERE MIXED and incubated WITH 20 MIKROLITER of a STOCK SOLUTION of the inhibitor 4B0 (10 MM 4B0 IN DMSO). 20 MICROLITERS OF the resulting solution WERE MIXED WITH 10 MICROLITERS OF RESERVOIR SOLUTION (900 MM LICL, 28 % (W/V) PEG 6000, 100 MM TRIS/HCL, PH 8.5) IN EACH WELL OF A CRYSTALLIZATION PLATE. A SINGLE MACROSEED, grown UNDER THE SAME CONDITIONS, WAS ADDED TO EACH DROPLET of the plate. THE DROPLETS WERE EQUILIBRATED AT 293.15 K using the sitting drop variant of the VAPOR DIFFUSION method. This procedure generated large single crystals of a CK2alpha'/4B0 complex. Afterwards, the inhibitor 4B0 was exchanged against THN27 by an extensive soaking procedure of several steps. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 18, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.03→46.293 Å / Num. obs: 179119 / % possible obs: 92.33 % / Redundancy: 3.4 % / Biso Wilson estimate: 12.33 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.05216 / Rpim(I) all: 0.0337 / Rrim(I) all: 0.06242 / Rsym value: 0.05216 / Net I/σ(I): 9.22 |
Reflection shell | Resolution: 1.03→1.067 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.9189 / Mean I/σ(I) obs: 1.02 / Num. unique obs: 17408 / CC1/2: 0.562 / Rpim(I) all: 0.5775 / Rrim(I) all: 1.089 / Rsym value: 0.9189 / % possible all: 90.48 |
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Processing
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.03→46.293 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 14.63 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.03→46.293 Å
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Refine LS restraints |
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LS refinement shell |
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