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Yorodumi- PDB-4kbk: CK1d in complex with (3S)-3-{4-[3-(4-fluorophenyl)-1-methyl-1H-py... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kbk | ||||||
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Title | CK1d in complex with (3S)-3-{4-[3-(4-fluorophenyl)-1-methyl-1H-pyrazol-4-yl]pyridin-2-yl}morpholine inhibitor | ||||||
Components | Casein kinase I isoform delta | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / ser/thr kinase / inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
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: 2.1 Å | ||||||
Authors | Liu, S. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2013 Title: Ligand-protein interactions of selective casein kinase 1 delta inhibitors. Authors: Mente, S. / Arnold, E. / Butler, T. / Chakrapani, S. / Chandrasekaran, R. / Cherry, K. / Dirico, K. / Doran, A. / Fisher, K. / Galatsis, P. / Green, M. / Hayward, M. / Humphrey, J. / ...Authors: Mente, S. / Arnold, E. / Butler, T. / Chakrapani, S. / Chandrasekaran, R. / Cherry, K. / Dirico, K. / Doran, A. / Fisher, K. / Galatsis, P. / Green, M. / Hayward, M. / Humphrey, J. / Knafels, J. / Li, J. / Liu, S. / Marconi, M. / McDonald, S. / Ohren, J. / Paradis, V. / Sneed, B. / Walton, K. / Wager, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kbk.cif.gz | 489.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kbk.ent.gz | 404 KB | Display | PDB format |
PDBx/mmJSON format | 4kbk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4kbk_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 4kbk_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 4kbk_validation.xml.gz | 48.4 KB | Display | |
Data in CIF | 4kbk_validation.cif.gz | 68 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kb/4kbk ftp://data.pdbj.org/pub/pdb/validation_reports/kb/4kbk | HTTPS FTP |
-Related structure data
Related structure data | 4kb8C 4kbaC 4kbcC 4kbh 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: 38537.223 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK1D, HCKID / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P48730, non-specific serine/threonine protein kinase, tau-protein kinase #2: Chemical | ChemComp-1QG / ( #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.66 % |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
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Detector | Type: ADSC QUANTUM 210 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. all: 72924 / Num. obs: 72584 / % possible obs: 95.6 % / Observed criterion σ(I): 2 / Redundancy: 2.38 % / Biso Wilson estimate: 31.97 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 12.14 |
-Processing
Software | Name: BUSTER / Version: 2.11.5 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→17.21 Å / Cor.coef. Fo:Fc: 0.9387 / Cor.coef. Fo:Fc free: 0.9147 / SU R Cruickshank DPI: 0.227 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 39.37 Å2
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Refine analyze | Luzzati coordinate error obs: 0.271 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→17.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.15 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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