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Open data
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Basic information
Entry | Database: PDB / ID: 8auy | ||||||
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Title | Small molecule stabilizer for ERalpha and 14-3-3 (1080298) | ||||||
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Function / homology | ![]() regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of epidermal cell division / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Visser, E.J. / Vandenboorn, E.M.F. / Ottmann, C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-Based Optimization of Covalent, Small-Molecule Stabilizers of the 14-3-3 sigma /ER alpha Protein-Protein Interaction from Nonselective Fragments. Authors: Konstantinidou, M. / Visser, E.J. / Vandenboorn, E. / Chen, S. / Jaishankar, P. / Overmans, M. / Dutta, S. / Neitz, R.J. / Renslo, A.R. / Ottmann, C. / Brunsveld, L. / Arkin, M.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 73.1 KB | Display | ![]() |
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PDB format | ![]() | 50.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8ai0C ![]() 8alrC ![]() 8altC ![]() 8alvC ![]() 8alwC ![]() 8am7C ![]() 8anfC ![]() 8aoyC ![]() 8apsC ![]() 8aq1C ![]() 8aqcC ![]() 8aqeC ![]() 8aqzC ![]() 8ar4C ![]() 8ar5C ![]() 8argC ![]() 8aroC ![]() 8arqC ![]() 8arrC ![]() 8arwC ![]() 8arxC ![]() 8aryC ![]() 8arzC ![]() 8as1C ![]() 8at9C ![]() 8atpC ![]() 8atrC ![]() 8atsC ![]() 8au2C ![]() 8ausC ![]() 8av3C ![]() 8av4C ![]() 8av7C ![]() 8av8C ![]() 8awgC ![]() 8axeC ![]() 8axuC ![]() 8azeC ![]() 8b39C ![]() 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: 613.596 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() | ||||||
#3: Chemical | #4: Chemical | ChemComp-O2X / ~{ | #5: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.54 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.095 M HEPES (pH 7.1), PEG400 (24 (v/v)), 0.19 M CaCl2 and 5% (v/v) Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.5→66.23 Å / Num. obs: 44445 / % possible obs: 96.3 % / Redundancy: 3.1 % / CC1/2: 0.928 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.5→1.53 Å / Num. unique obs: 2208 / CC1/2: 0.404 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4JC3 Resolution: 1.5→66.23 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.929 / SU B: 1.501 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.597 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→66.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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