+Open data
-Basic information
Entry | Database: PDB / ID: 6yum | ||||||
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Title | CK2 alpha bound to unclosed Macrocycle | ||||||
Components | Casein kinase II subunit alphaCasein kinase 2 | ||||||
Keywords | TRANSFERASE / Kinase / Macrocycle / Inhibitor / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information regulation of chromosome separation / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Sin3-type complex / Receptor Mediated Mitophagy / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of apoptotic signaling pathway ...regulation of chromosome separation / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Sin3-type complex / Receptor Mediated Mitophagy / Synthesis of PC / 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 / chaperone-mediated protein folding / negative regulation of ubiquitin-dependent protein catabolic process / Signal transduction by L1 / peptidyl-threonine phosphorylation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Hsp90 protein binding / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / positive regulation of protein catabolic process / rhythmic process / KEAP1-NFE2L2 pathway / double-strand break repair / kinase activity / positive regulation of cell growth / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / negative regulation of translation / protein stabilization / 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 / nucleus / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Kraemer, A. / Hanke, T. / Kurz, C. / Celik, I. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Eur.J.Med.Chem. / Year: 2020 Title: Optimization of pyrazolo[1,5-a]pyrimidines lead to the identification of a highly selective casein kinase 2 inhibitor. Authors: Kramer, A. / Kurz, C.G. / Berger, B.T. / Celik, I.E. / Tjaden, A. / Greco, F.A. / Knapp, S. / Hanke, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yum.cif.gz | 153 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yum.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6yum.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yu/6yum ftp://data.pdbj.org/pub/pdb/validation_reports/yu/6yum | HTTPS FTP |
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-Related structure data
Related structure data | 6yulC 3pe2S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain: (Details: Chains A G) |
-Components
#1: Protein | Mass: 45208.559 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 | ChemComp-SO4 / #3: Chemical | #4: 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: 2.71 Å3/Da / Density % sol: 54.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M MES pH 6.5 0.2 ammonia sulphate 30% PEG 5000 MME 10 mg/mL protein |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000031 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.000031 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→44.36 Å / Num. obs: 26481 / % possible obs: 99.9 % / Redundancy: 9.6 % / CC1/2: 0.998 / Rpim(I) all: 0.045 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.75→2.9 Å / Num. unique obs: 3806 / CC1/2: 0.923 / Rpim(I) all: 0.316 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3PE2 Resolution: 2.75→44.36 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.918 / SU B: 21.771 / SU ML: 0.397 / Cross valid method: FREE R-VALUE / ESU R: 0.938 / ESU R Free: 0.37 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.329 Å2
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Refinement step | Cycle: LAST / Resolution: 2.75→44.36 Å
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Refine LS restraints |
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LS refinement shell |
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