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Open data
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Basic information
Entry | Database: PDB / ID: 8a62 | ||||||
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Title | Small molecule stabilizer (compound 2) for FOXO1 and 14-3-3 | ||||||
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![]() | STRUCTURAL PROTEIN / 14-3-3 / FOXO1 / Stabilization | ||||||
Function / homology | ![]() cellular response to hyperoxia / regulation of transcription initiation by RNA polymerase II / AKT-mediated inactivation of FOXO1A / FOXO-mediated transcription of cell cycle genes / AKT phosphorylates targets in the nucleus / positive regulation of smooth muscle cell apoptotic process / neuronal stem cell population maintenance / regulation of neural precursor cell proliferation / response to fatty acid / Regulation of FOXO transcriptional activity by acetylation ...cellular response to hyperoxia / regulation of transcription initiation by RNA polymerase II / AKT-mediated inactivation of FOXO1A / FOXO-mediated transcription of cell cycle genes / AKT phosphorylates targets in the nucleus / positive regulation of smooth muscle cell apoptotic process / neuronal stem cell population maintenance / regulation of neural precursor cell proliferation / response to fatty acid / Regulation of FOXO transcriptional activity by acetylation / regulation of reactive oxygen species metabolic process / negative regulation of stress-activated MAPK cascade / negative regulation of cardiac muscle hypertrophy in response to stress / cellular response to cold / FOXO-mediated transcription of cell death genes / temperature homeostasis / negative regulation of fat cell differentiation / protein acetylation / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / fat cell differentiation / blood vessel development / intracellular glucose homeostasis / Constitutive Signaling by AKT1 E17K in Cancer / Regulation of gene expression in beta cells / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / cellular response to nitric oxide / canonical Wnt signaling pathway / negative regulation of keratinocyte proliferation / establishment of skin barrier / negative regulation of insulin secretion / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / positive regulation of autophagy / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / negative regulation of stem cell proliferation / energy homeostasis / RHO GTPases activate PKNs / positive regulation of gluconeogenesis / protein sequestering activity / protein kinase A signaling / negative regulation of innate immune response / protein export from nucleus / cellular response to starvation / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / stem cell proliferation / protein phosphatase 2A binding / Translocation of SLC2A4 (GLUT4) to the plasma membrane / promoter-specific chromatin binding / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / MAPK6/MAPK4 signaling / negative regulation of canonical Wnt signaling pathway / chromatin DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / beta-catenin binding / autophagy / positive regulation of protein catabolic process / cellular response to insulin stimulus / intrinsic apoptotic signaling pathway in response to DNA damage / protein localization / insulin receptor signaling pathway / gene expression / cellular response to oxidative stress / positive regulation of cell growth / DNA-binding transcription activator activity, RNA polymerase II-specific / Interleukin-4 and Interleukin-13 signaling / sequence-specific DNA binding / nucleic acid binding / regulation of cell cycle / DNA-binding transcription factor activity, RNA polymerase II-specific / cadherin binding / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / DNA damage response / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / apoptotic process / protein kinase binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular space / extracellular exosome Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kenanova, D.N. / Visser, E.J. / Virta, J. / Sijbesma, E. / Centorrino, F. / Zhong, M. / Vickery, H. / Neitz, J. / Brunsveld, L. / Ottmann, C. / Arkin, M.R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A Systematic Approach to the Discovery of Protein-Protein Interaction Stabilizers. Authors: Kenanova, D.N. / Visser, E.J. / Virta, J.M. / Sijbesma, E. / Centorrino, F. / Vickery, H.R. / Zhong, M. / Neitz, R.J. / Brunsveld, L. / Ottmann, C. / 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 | ![]() | 114.7 KB | Display | ![]() |
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PDB format | ![]() | 87 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8a65C ![]() 8a68C ![]() 8a6fC ![]() 8a6hC ![]() 8admC ![]() 8afnC ![]() 8av0C ![]() 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
#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: 1388.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() | ||||||
#3: Chemical | #4: Chemical | ChemComp-L7L / ( | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.85 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.095 M HEPES pH 7.5, 0.19 M CaCl2, 5% glycerol, 24% PEG 400 |
-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: 1.03322 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→45.41 Å / Num. obs: 512777 / % possible obs: 97.6 % / Redundancy: 13.8 % / CC1/2: 1 / Net I/σ(I): 39 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 12.6 % / Num. unique obs: 1773 / CC1/2: 0.992 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4JC3 Resolution: 1.6→45.41 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.03 / 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: 59.7 Å2 / Biso mean: 17.2806 Å2 / Biso min: 1.58 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→45.41 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26
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