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Yorodumi- PDB-5mqv: Crystal structure of human Casein Kinase I delta in complex with ... -
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-Basic information
Entry | Database: PDB / ID: 5mqv | ||||||
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Title | Crystal structure of human Casein Kinase I delta in complex with 4-(2,5-Dimethoxyphenyl)-N-(4-(5-(4-fluorphenyl)-2-(methylthio)-1H-imidazol-4-yl)-pyridin-2-yl)-1-methyl-1H-pyrrole-2-carboxamide | ||||||
Components | Casein kinase I isoform delta | ||||||
Keywords | TRANSFERASE / CK1D / Kinase-inhibitor complex / Kinase | ||||||
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 / spindle assembly / Major pathway of rRNA processing in the nucleolus and cytosol / 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 / spindle microtubule / circadian regulation of gene expression / regulation of circadian rhythm / Wnt signaling pathway / spindle / endocytosis / Regulation of PLK1 Activity at G2/M Transition / positive regulation of canonical Wnt signaling pathway / Circadian Clock / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / 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: 2.154 Å | ||||||
Authors | Pichlo, C. / Brunstein, E. / Baumann, U. | ||||||
Citation | Journal: Molecules / Year: 2017 Title: Optimized 4,5-Diarylimidazoles as Potent/Selective Inhibitors of Protein Kinase CK1 delta and Their Structural Relation to p38 alpha MAPK. Authors: Halekotte, J. / Witt, L. / Ianes, C. / Kruger, M. / Buhrmann, M. / Rauh, D. / Pichlo, C. / Brunstein, E. / Luxenburger, A. / Baumann, U. / Knippschild, U. / Bischof, J. / Peifer, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mqv.cif.gz | 1016.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mqv.ent.gz | 865.7 KB | Display | PDB format |
PDBx/mmJSON format | 5mqv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mq/5mqv ftp://data.pdbj.org/pub/pdb/validation_reports/mq/5mqv | HTTPS FTP |
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-Related structure data
Related structure data | 5ml5C 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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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 36377.887 Da / Num. of mol.: 6 / Fragment: kinase domain Source method: isolated from a genetically manipulated source Details: CSNK1D 1-294 with N-terminal thrombin cleavage site and polyHis-tag Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK1D, HCKID / Plasmid: CK1D / 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-D5Q / #3: Chemical | ChemComp-PO4 / #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: 4.09 Å3/Da / Density % sol: 69.94 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Hepes pH 7.0, 0.7 M NaH2PO4, 0.7 M KH2PO4 |
-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 22, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.154→49.291 Å / Num. obs: 187597 / % possible obs: 99 % / Redundancy: 4.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.068 / Net I/σ(I): 14.76 |
Reflection shell | Resolution: 2.154→2.231 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.49 / Num. unique all: 17796 / CC1/2: 0.828 / Rrim(I) all: 0.51 / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4TWC Resolution: 2.154→49.291 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.79 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 282.11 Å2 / Biso mean: 57.0082 Å2 / Biso min: 19.85 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.154→49.291 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28
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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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