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Open data
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Basic information
Entry | Database: PDB / ID: 6gzm | ||||||
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Title | Crystal Structure of Human CKIdelta with A86 | ||||||
![]() | Casein kinase I isoform delta | ||||||
![]() | TRANSFERASE / CDK9 / kinase inhibitor / A86 | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ben-neriah, Y. / Venkatachalam, A. / Minzel, W. / Fink, A. / Snir-Alkalay, I. / Vacca, J. | ||||||
![]() | ![]() Title: Small Molecules Co-targeting CKI alpha and the Transcriptional Kinases CDK7/9 Control AML in Preclinical Models. Authors: Minzel, W. / Venkatachalam, A. / Fink, A. / Hung, E. / Brachya, G. / Burstain, I. / Shaham, M. / Rivlin, A. / Omer, I. / Zinger, A. / Elias, S. / Winter, E. / Erdman, P.E. / Sullivan, R.W. / ...Authors: Minzel, W. / Venkatachalam, A. / Fink, A. / Hung, E. / Brachya, G. / Burstain, I. / Shaham, M. / Rivlin, A. / Omer, I. / Zinger, A. / Elias, S. / Winter, E. / Erdman, P.E. / Sullivan, R.W. / Fung, L. / Mercurio, F. / Li, D. / Vacca, J. / Kaushansky, N. / Shlush, L. / Oren, M. / Levine, R. / Pikarsky, E. / Snir-Alkalay, I. / Ben-Neriah, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 162.4 KB | Display | ![]() |
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PDB format | ![]() | 127.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 36.2 KB | Display | |
Data in CIF | ![]() | 55 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6gzdC ![]() 6gzhC ![]() 3uytS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34310.613 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P48730, non-specific serine/threonine protein kinase, tau-protein kinase #2: Chemical | ChemComp-CIT / | #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.32 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: The construct used for crystallization was that of the wild type protein with the mutation R13N. Crystals of CK1d in complex with A-86 were obtained using hanging drop vapour diffusion set- ...Details: The construct used for crystallization was that of the wild type protein with the mutation R13N. Crystals of CK1d in complex with A-86 were obtained using hanging drop vapour diffusion set-ups. CK1d at a concentration of 13.6 mg/ml (50 mM HEPES, 266 mM NaCl, 1 mM EDTA, 1 mM DTT, 5 mM B-OG, pH 7.5) was pre-incubated with 2 mM (5.1-fold molar excess) of A-86 (150 mM in DMSO) for 1 h. 1 ul of the protein solution was then mixed with 1 ul of reservoir solution (0.1 M Na3-Citrate, pH 4.9, 18 %(w/v) PEG 3350) and equilibrated at 20 C over 0.4 ml of reservoir solution. Well diffracting crystals appeared over night |
-Data collection
Diffraction | Mean temperature: 110.15 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→29.19 Å / Num. obs: 80180 / % possible obs: 96.5 % / Redundancy: 2.4 % / Rrim(I) all: 0.09 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 1.59→1.68 Å / Redundancy: 2.4 % / Num. unique obs: 11624 / Rrim(I) all: 0.57 / % possible all: 96.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3uyt Resolution: 1.59→29.19 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.08 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.076 Å2
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Refinement step | Cycle: 1 / Resolution: 1.59→29.19 Å
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