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- PDB-7bg3: 14-3-3 sigma with Pin1 binding site pS72 and covalently bound PC2046 -
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Open data
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Basic information
Entry | Database: PDB / ID: 7bg3 | |||||||||
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Title | 14-3-3 sigma with Pin1 binding site pS72 and covalently bound PC2046 | |||||||||
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![]() | PEPTIDE BINDING PROTEIN / 1433 / Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 | |||||||||
Function / homology | ![]() cis-trans isomerase activity / phosphothreonine residue binding / negative regulation of cell motility / ubiquitin ligase activator activity / regulation of protein localization to nucleus / GTPase activating protein binding / mitogen-activated protein kinase kinase binding / regulation of mitotic nuclear division / postsynaptic cytosol / negative regulation of SMAD protein signal transduction ...cis-trans isomerase activity / phosphothreonine residue binding / negative regulation of cell motility / ubiquitin ligase activator activity / regulation of protein localization to nucleus / GTPase activating protein binding / mitogen-activated protein kinase kinase binding / regulation of mitotic nuclear division / postsynaptic cytosol / negative regulation of SMAD protein signal transduction / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / PI5P Regulates TP53 Acetylation / negative regulation of amyloid-beta formation / cytoskeletal motor activity / protein peptidyl-prolyl isomerization / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / RHO GTPases Activate NADPH Oxidases / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / negative regulation of stem cell proliferation / : / RHO GTPases activate PKNs / protein sequestering activity / protein kinase A signaling / negative regulation of innate immune response / protein export from nucleus / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / ciliary basal body / positive regulation of protein export from nucleus / positive regulation of GTPase activity / regulation of cytokinesis / stem cell proliferation / negative regulation of protein binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Negative regulators of DDX58/IFIH1 signaling / TP53 Regulates Metabolic Genes / phosphoprotein binding / synapse organization / negative regulation of transforming growth factor beta receptor signaling pathway / regulation of protein phosphorylation / negative regulation of protein kinase activity / regulation of protein stability / tau protein binding / negative regulation of protein catabolic process / neuron differentiation / negative regulation of ERK1 and ERK2 cascade / ISG15 antiviral mechanism / beta-catenin binding / intrinsic apoptotic signaling pathway in response to DNA damage / protein localization / positive regulation of canonical Wnt signaling pathway / positive regulation of protein binding / midbody / positive regulation of cell growth / regulation of gene expression / Regulation of TP53 Activity through Phosphorylation / response to hypoxia / protein stabilization / regulation of cell cycle / nuclear speck / cadherin binding / positive regulation of protein phosphorylation / glutamatergic synapse / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Wolter, M. / Dijck, L.v. / Cossar, P.J. / Ottmann, C. | |||||||||
Funding support | 2items
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![]() | ![]() Title: Reversible Covalent Imine-Tethering for Selective Stabilization of 14-3-3 Hub Protein Interactions. Authors: Cossar, P.J. / Wolter, M. / van Dijck, L. / Valenti, D. / Levy, L.M. / Ottmann, C. / Brunsveld, L. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.6 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 | ![]() 7aogSC ![]() 7axnC ![]() 7ayfC ![]() 7az1C ![]() 7az2C ![]() 7bdpC ![]() 7bdtC ![]() 7bdyC ![]() 7bfwC ![]() 7bgqC ![]() 7bgrC ![]() 7bgvC ![]() 7bgwC ![]() 7nifC ![]() 7nigC ![]() 7nixC ![]() 7nj6C ![]() 7nj8C ![]() 7njaC ![]() 7nqpC ![]() 7nrkC ![]() 7nrlC ![]() 7nsvC 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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1 | ![]()
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Unit cell |
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Components
-Protein / Protein/peptide , 2 types, 2 molecules AP
#1: Protein | Mass: 28169.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 2195.378 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Non-polymers , 4 types, 312 molecules ![](data/chem/img/TKK.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-TKK / |
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#4: Chemical | ChemComp-CA / |
#5: Chemical | ChemComp-CL / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.39 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.1 Details: 0.095 M HEPES Na pH 7.1, 27% PEG400, 0.19M Calcium chloride, 5% Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 12, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.4→66.29 Å / Num. obs: 57149 / % possible obs: 99.6 % / Redundancy: 12.1 % / Biso Wilson estimate: 15.87 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.016 / Rrim(I) all: 0.058 / Net I/σ(I): 21.7 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7AOG Resolution: 1.4→56.103 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.85 / 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: 81.79 Å2 / Biso mean: 21.5251 Å2 / Biso min: 9.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.4→56.103 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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