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Open data
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Basic information
Entry | Database: PDB / ID: 8btq | ||||||
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Title | Small molecule stabilizer for 14-3-3/ChREBP (Cmd1-soaking) | ||||||
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Function / homology | ![]() carbohydrate response element binding / glucose mediated signaling pathway / AMPK inhibits chREBP transcriptional activation activity / PKA-mediated phosphorylation of key metabolic factors / PP2A-mediated dephosphorylation of key metabolic factors / positive regulation of transcription from RNA polymerase II promoter by glucose / ChREBP activates metabolic gene expression / positive regulation of fatty acid biosynthetic process / negative regulation of oxidative phosphorylation / triglyceride homeostasis ...carbohydrate response element binding / glucose mediated signaling pathway / AMPK inhibits chREBP transcriptional activation activity / PKA-mediated phosphorylation of key metabolic factors / PP2A-mediated dephosphorylation of key metabolic factors / positive regulation of transcription from RNA polymerase II promoter by glucose / ChREBP activates metabolic gene expression / positive regulation of fatty acid biosynthetic process / negative regulation of oxidative phosphorylation / triglyceride homeostasis / lipid biosynthetic process / DNA-binding transcription activator activity / regulation of epidermal cell division / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pennings, M.A.M. / Visser, E.J. / Ottmann, C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular glues of the regulatory ChREBP/14-3-3 complex protect beta cells from glucolipotoxicity. Authors: Katz, L.S. / Visser, E.J. / Plitzko, K.F. / Pennings, M. / Cossar, P.J. / Tse, I.L. / Kaiser, M. / Brunsveld, L. / Scott, D.K. / Ottmann, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 76.4 KB | Display | ![]() |
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PDB format | ![]() | 53.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8bweC ![]() 8bwhC ![]() 8c1yC ![]() 4jc3S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 26542.914 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() | ||||||
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#2: Protein/peptide | ![]() Mass: 2482.883 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() | ||||||
#3: Chemical | #4: Chemical | ChemComp-OQE / [ | #5: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.79 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.095 M HEPES pH = 7.5 27% PEG400 0.19 M CaCl2 5% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 4, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.6→45.41 Å / Num. obs: 38129 / % possible obs: 99.9 % / Redundancy: 12.9 % / CC1/2: 0.999 / Net I/σ(I): 26 |
Reflection shell | Resolution: 1.6→1.63 Å / Num. unique obs: 1837 / CC1/2: 0.959 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4JC3 Resolution: 1.6→45.41 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.523 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.901 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→45.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 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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