+Open data
-Basic information
Entry | Database: PDB / ID: 6l20 | ||||||
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Title | Crystal structure of CK2a2 with hematein | ||||||
Components | Casein kinase II subunit alpha' | ||||||
Keywords | TRANSFERASE / protein kinase / inhibitor / complex | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.08735128172 Å | ||||||
Authors | Tsuyuguchi, M. / Kinoshita, T. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6l20.cif.gz | 295 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l20.ent.gz | 219.3 KB | Display | PDB format |
PDBx/mmJSON format | 6l20.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6l20_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6l20_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6l20_validation.xml.gz | 49.7 KB | Display | |
Data in CIF | 6l20_validation.cif.gz | 66.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l2/6l20 ftp://data.pdbj.org/pub/pdb/validation_reports/l2/6l20 | HTTPS FTP |
-Related structure data
Related structure data | 6l1zC 6l21C 6l22C 6l23C 6l24C 3e3bS 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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Unit cell |
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-Components
#1: Protein | Mass: 40031.855 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A2, CK2A2 / Production host: Escherichia coli (E. coli) References: UniProt: P19784, non-specific serine/threonine protein kinase #2: Chemical | ChemComp-E3U / ( #3: Chemical | 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: 2.43 Å3/Da / Density % sol: 49.38 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: PEG 8000 |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jan 26, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.087→50 Å / Num. obs: 27801 / % possible obs: 91.4 % / Redundancy: 1.9 % / Biso Wilson estimate: 48.1788392164 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 3.09→3.14 Å / Rmerge(I) obs: 0.409 / Num. unique obs: 3582 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3E3B Resolution: 3.08735128172→35.0407993379 Å / SU ML: 0.506177809973 / Cross valid method: FREE R-VALUE / σ(F): 1.97272291486 / Phase error: 44.3696565227
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.8544976382 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.08735128172→35.0407993379 Å
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Refine LS restraints |
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LS refinement shell |
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