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Yorodumi- PDB-6f26: Crystal structure of human Casein Kinase I delta in complex with ... -
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-Basic information
Entry | Database: PDB / ID: 6f26 | ||||||
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Title | Crystal structure of human Casein Kinase I delta in complex with compound 31b | ||||||
Components | Casein kinase I isoform delta | ||||||
Keywords | TRANSFERASE / Kinase / Inhibitor / Complex / CK1 | ||||||
Function / homology | Function and homology information positive regulation of non-canonical Wnt signaling pathway / protein localization to Golgi apparatus / midbrain dopaminergic neuron differentiation / COPII vesicle coating / microtubule nucleation / tau-protein kinase / non-motile cilium assembly / protein localization to cilium / protein localization to centrosome / COPII-mediated vesicle transport ...positive regulation of non-canonical Wnt signaling pathway / protein localization to Golgi apparatus / midbrain dopaminergic neuron differentiation / COPII vesicle coating / microtubule nucleation / tau-protein kinase / non-motile cilium assembly / protein localization to cilium / protein localization to centrosome / COPII-mediated vesicle transport / tau-protein kinase activity / Golgi organization / Major pathway of rRNA processing in the nucleolus and cytosol / spindle assembly / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / endoplasmic reticulum-Golgi intermediate compartment membrane / AURKA Activation by TPX2 / cellular response to nerve growth factor stimulus / ciliary basal body / circadian regulation of gene expression / spindle microtubule / regulation of circadian rhythm / Wnt signaling pathway / spindle / endocytosis / Regulation of PLK1 Activity at G2/M Transition / Circadian Clock / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of canonical Wnt signaling pathway / non-specific serine/threonine protein kinase / protein kinase activity / cadherin binding / positive regulation of protein phosphorylation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å | ||||||
Authors | Pichlo, C. / Brunstein, E. / Baumann, U. | ||||||
Citation | Journal: Molecules / Year: 2019 Title: Design, Synthesis and Biological Evaluation of Isoxazole-Based CK1 Inhibitors Modified with Chiral Pyrrolidine Scaffolds. Authors: Luxenburger, A. / Schmidt, D. / Ianes, C. / Pichlo, C. / Kruger, M. / von Drathen, T. / Brunstein, E. / Gainsford, G.J. / Baumann, U. / Knippschild, U. / Peifer, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6f26.cif.gz | 351.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f26.ent.gz | 292.9 KB | Display | PDB format |
PDBx/mmJSON format | 6f26.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6f26_validation.pdf.gz | 981.1 KB | Display | wwPDB validaton report |
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Full document | 6f26_full_validation.pdf.gz | 986.4 KB | Display | |
Data in XML | 6f26_validation.xml.gz | 26.7 KB | Display | |
Data in CIF | 6f26_validation.cif.gz | 37.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f2/6f26 ftp://data.pdbj.org/pub/pdb/validation_reports/f2/6f26 | HTTPS FTP |
-Related structure data
Related structure data | 6f1wC 4twcS 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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-Components
#1: Protein | Mass: 36377.887 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK1D, HCKID / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): TAKARA 2 References: UniProt: P48730, non-specific serine/threonine protein kinase, tau-protein kinase #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.53 Å3/Da / Density % sol: 51.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1 M MES pH 5.5, 10 % (w/v) PEG 4000, 0.2 M lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 21, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→47.651 Å / Num. obs: 63861 / % possible obs: 99 % / Redundancy: 5 % / Net I/σ(I): 13.12 |
Reflection shell | Resolution: 1.83→1.895 Å / Mean I/σ(I) obs: 2.41 / Num. unique obs: 4416 / CC1/2: 0.785 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4TWC Resolution: 1.83→47.651 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 21.33 / 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: 1.83→47.651 Å
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Refine LS restraints |
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LS refinement shell |
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