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Open data
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Basic information
Entry | Database: PDB / ID: 8bi7 | ||||||
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Title | Binary structure of 14-3-3s and PKR phosphopeptide | ||||||
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![]() | PEPTIDE BINDING PROTEIN / 14-3-3 / hub-protein / phosphopeptide | ||||||
Function / homology | ![]() regulation of NLRP3 inflammasome complex assembly / Inhibition of PKR / eukaryotic translation initiation factor 2alpha kinase activity / response to interferon-alpha / negative regulation of osteoblast proliferation / regulation of hematopoietic progenitor cell differentiation / positive regulation of stress-activated MAPK cascade / protein phosphatase regulator activity / SUMOylation of immune response proteins / regulation of hematopoietic stem cell proliferation ...regulation of NLRP3 inflammasome complex assembly / Inhibition of PKR / eukaryotic translation initiation factor 2alpha kinase activity / response to interferon-alpha / negative regulation of osteoblast proliferation / regulation of hematopoietic progenitor cell differentiation / positive regulation of stress-activated MAPK cascade / protein phosphatase regulator activity / SUMOylation of immune response proteins / regulation of hematopoietic stem cell proliferation / regulation of hematopoietic stem cell differentiation / negative regulation of viral genome replication / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / antiviral innate immune response / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / 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 / positive regulation of chemokine production / endoplasmic reticulum unfolded protein response / RHO GTPases activate PKNs / protein kinase A signaling / protein sequestering activity / cellular response to amino acid starvation / negative regulation of innate immune response / protein export from nucleus / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of protein export from nucleus / release of cytochrome c from mitochondria / stem cell proliferation / positive regulation of cytokine production / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / non-specific protein-tyrosine kinase / negative regulation of protein kinase activity / non-membrane spanning protein tyrosine kinase activity / response to virus / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / PKR-mediated signaling / Evasion by RSV of host interferon responses / ISG15 antiviral mechanism / positive regulation of non-canonical NF-kappaB signal transduction / intrinsic apoptotic signaling pathway in response to DNA damage / Interferon alpha/beta signaling / double-stranded RNA binding / kinase activity / positive regulation of NF-kappaB transcription factor activity / positive regulation of cell growth / defense response to virus / positive regulation of MAPK cascade / protein autophosphorylation / negative regulation of translation / non-specific serine/threonine protein kinase / ribosome / regulation of cell cycle / protein kinase activity / cadherin binding / translation / negative regulation of cell population proliferation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / signal transduction / RNA binding / extracellular space / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Somsen, B.A. / Ottmann, C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Reversible Dual-Covalent Molecular Locking of the 14-3-3/ERR gamma Protein-Protein Interaction as a Molecular Glue Drug Discovery Approach. Authors: Somsen, B.A. / Schellekens, R.J.C. / Verhoef, C.J.A. / Arkin, M.R. / Ottmann, C. / Cossar, P.J. / 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 | ![]() | 74.2 KB | Display | ![]() |
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PDB format | ![]() | 52.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.8 KB | Display | ![]() |
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Full document | ![]() | 434.2 KB | Display | |
Data in XML | ![]() | 14.3 KB | Display | |
Data in CIF | ![]() | 22.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8b2iC ![]() 8b2kC ![]() 8b4qC ![]() 8b5pC ![]() 8bfcC ![]() 8bjgC ![]() 8bjnC ![]() 8bm5C ![]() 6y1dS 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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Components
#1: Protein | Mass: 26542.914 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: GAMGS at the beginning (-5 to -1) are part of the expression tag Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Protein/peptide | Mass: 1412.465 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() References: UniProt: P19525, non-specific serine/threonine protein kinase, non-specific protein-tyrosine kinase | ||||
#3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.82 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.095 M Hepes pH 7.1, 0.19 M CaCl2, 25% PEG400, 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: Apr 6, 2022 |
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→45.64 Å / Num. obs: 742644 / % possible obs: 99.7 % / Redundancy: 12.9 % / CC1/2: 0.999 / Net I/σ(I): 36.4 |
Reflection shell | Resolution: 1.4→1.43 Å / Mean I/σ(I) obs: 7.1 / Num. unique obs: 33081 / CC1/2: 0.984 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6y1d Resolution: 1.4→45.64 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 17.44 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→45.64 Å
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Refine LS restraints |
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LS refinement shell |
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