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- PDB-7orh: Ternary complex of 14-3-3 sigma, p27pT198 phosphopeptide, and WQ178 -
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Open data
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Basic information
Entry | Database: PDB / ID: 7orh | ||||||
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Title | Ternary complex of 14-3-3 sigma, p27pT198 phosphopeptide, and WQ178 | ||||||
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![]() | SIGNALING PROTEIN / protein-peptide complex small-molecule | ||||||
Function / homology | ![]() cyclin-dependent protein kinase activating kinase regulator activity / regulation of lens fiber cell differentiation / negative regulation of cardiac muscle tissue regeneration / negative regulation of cyclin-dependent protein kinase activity / PTK6 Regulates Cell Cycle / autophagic cell death / FOXO-mediated transcription of cell cycle genes / negative regulation of epithelial cell proliferation involved in prostate gland development / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / p53-Dependent G1 DNA Damage Response ...cyclin-dependent protein kinase activating kinase regulator activity / regulation of lens fiber cell differentiation / negative regulation of cardiac muscle tissue regeneration / negative regulation of cyclin-dependent protein kinase activity / PTK6 Regulates Cell Cycle / autophagic cell death / FOXO-mediated transcription of cell cycle genes / negative regulation of epithelial cell proliferation involved in prostate gland development / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / p53-Dependent G1 DNA Damage Response / regulation of cell cycle G1/S phase transition / regulation of exit from mitosis / epithelial cell proliferation involved in prostate gland development / negative regulation of epithelial cell apoptotic process / negative regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of phosphorylation / ubiquitin ligase activator activity / cyclin-dependent protein serine/threonine kinase inhibitor activity / negative regulation of vascular associated smooth muscle cell proliferation / RHO GTPases activate CIT / nuclear export / negative regulation of mitotic cell cycle / AKT phosphorylates targets in the cytosol / Cul4A-RING E3 ubiquitin ligase complex / epithelial cell apoptotic process / cellular response to antibiotic / Cyclin E associated events during G1/S transition / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / negative regulation of kinase activity / regulation of cyclin-dependent protein serine/threonine kinase activity / molecular function inhibitor activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / cellular response to lithium ion / positive regulation of DNA replication / regulation of epidermal cell division / protein kinase C inhibitor activity / protein kinase inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / Cyclin A:Cdk2-associated events at S phase entry / Constitutive Signaling by AKT1 E17K in Cancer / regulation of G1/S transition of mitotic cell cycle / inner ear development / Regulation of localization of FOXO transcription factors / cellular response to organic cyclic compound / keratinocyte proliferation / cyclin binding / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / response to amino acid / establishment of skin barrier / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / response to glucose / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / response to cadmium ion / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / negative regulation of stem cell proliferation / RHO GTPases activate PKNs / Notch signaling pathway / positive regulation of microtubule polymerization / protein sequestering activity / protein kinase A signaling / Hsp70 protein binding / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / FLT3 Signaling / negative regulation of innate immune response / protein export from nucleus / regulation of cell migration / potassium ion transport / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / DNA Damage/Telomere Stress Induced Senescence / stem cell proliferation / placenta development / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / SCF(Skp2)-mediated degradation of p27/p21 / sensory perception of sound / negative regulation of protein kinase activity / Cyclin D associated events in G1 / G1/S transition of mitotic cell cycle / cellular senescence / negative regulation of cell growth / response to peptide hormone / positive regulation of protein catabolic process / intrinsic apoptotic signaling pathway in response to DNA damage / protein localization / response to estradiol / Senescence-Associated Secretory Phenotype (SASP) / cellular response to hypoxia / heart development / positive regulation of cell growth / protein-folding chaperone binding / protein phosphatase binding / endosome / molecular adaptor activity / regulation of cell cycle Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Centorrino, F. / Wu, Q. / Ottmann, C. | ||||||
Funding support | European Union, 1items
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![]() | ![]() Title: A crystallography-based study of fragment extensions into the 14-3-3 binding groove Authors: Centorrino, F. / Wu, Q. / Cossar, P. / Brunsveld, L. / 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 | ![]() | 135 KB | Display | ![]() |
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PDB format | ![]() | 85.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1011.1 KB | Display | ![]() |
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Full document | ![]() | 1014.3 KB | Display | |
Data in XML | ![]() | 14.6 KB | Display | |
Data in CIF | ![]() | 21.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7opwC ![]() 7oq7C ![]() 7oq8C ![]() 7oq9C ![]() 7oqaC ![]() 7oqgC ![]() 7oqjC ![]() 7oqsC ![]() 7oquC ![]() 7oqwC ![]() 7or3C ![]() 7or5C ![]() 7or7C ![]() 7or8C ![]() 7orgC ![]() 7orsC ![]() 7ortC ![]() 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
-Protein / Protein/peptide , 2 types, 2 molecules AP
#1: Protein | Mass: 28226.518 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1522.712 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Non-polymers , 4 types, 299 molecules ![](data/chem/img/0B7.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.84 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 0.095 M Hepes pH7.3, 26%PEG 400, 0.19 M CaCl2, and 5 % Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54187 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Feb 22, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54187 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→41.53 Å / Num. obs: 26790 / % possible obs: 99.7 % / Redundancy: 6.1 % / Biso Wilson estimate: 13.12 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.106 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1291 / CC1/2: 0.874 / % possible all: 95.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4jc3 Resolution: 1.8→41.53 Å / SU ML: 0.1816 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.0666 / Stereochemistry target values: GeoStd + Monomer Library
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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 mean: 17.11 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→41.53 Å
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Refine LS restraints |
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LS refinement shell |
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