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- PDB-6y7t: Engineered conjugation of lysine-specific molecular tweezers with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6y7t | |||||||||
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Title | Engineered conjugation of lysine-specific molecular tweezers with ExoS derived peptidic inhibitor enhance affinity towards target protein 14-3-3 through ditopic binding | |||||||||
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![]() | PEPTIDE BINDING PROTEIN / Protein-protein interactions / supramolecular ligands / molecular tweezers / protein recognition / hybrid ligands | |||||||||
Function / homology | ![]() regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / NAD+-protein poly-ADP-ribosyltransferase activity / phosphoserine residue binding / Activation of BAD and translocation to mitochondria ...regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / NAD+-protein poly-ADP-ribosyltransferase activity / 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 / RHO GTPases activate PKNs / protein kinase A signaling / protein sequestering activity / negative regulation of innate immune response / protein export from nucleus / nucleotidyltransferase activity / GTPase activator activity / 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 / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / intrinsic apoptotic signaling pathway in response to DNA damage / toxin activity / positive regulation of cell growth / regulation of cell cycle / cadherin binding / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular exosome / extracellular region / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Guillory, X. / Ottmann, C. | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Supramolecular Enhancement of a Natural 14-3-3 Protein Ligand. Authors: Guillory, X. / Hadrovic, I. / de Vink, P.J. / Sowislok, A. / Brunsveld, L. / Schrader, T. / Ottmann, C. #1: ![]() Title: The Molecular Tweezer CLR01 Stabilizes a Disordered Protein-Protein Interface. Authors: Bier, D. / Mittal, S. / Bravo-Rodriguez, K. / Sowislok, A. / Guillory, X. / Briels, J. / Heid, C. / Bartel, M. / Wettig, B. / Brunsveld, L. / Sanchez-Garcia, E. / Schrader, T. / Ottmann, C. #2: ![]() Title: Molecular tweezers modulate 14-3-3 protein-protein interactions. Authors: Bier, D. / Rose, R. / Bravo-Rodriguez, K. / Bartel, M. / Ramirez-Anguita, J.M. / Dutt, S. / Wilch, C. / Klarner, F.G. / Sanchez-Garcia, E. / Schrader, T. / 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 | ![]() | 389.8 KB | Display | ![]() |
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PDB format | ![]() | 320.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 39 KB | Display | |
Data in CIF | ![]() | 55.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4n7gS S: Starting model for refinement |
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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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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
-Protein / Protein/peptide , 2 types, 6 molecules AFKPDE
#1: Protein | Mass: 28226.518 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 1115.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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-Non-polymers , 4 types, 376 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/TWZ.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/TWZ.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-NA / #4: Chemical | #5: Chemical | #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: 3.54 Å3/Da / Density % sol: 65.21 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Bis-Tris Propane 0.2M sodium acetate trihydrate 20% PEG1000 10% Glycerol pH 7 Grew at 4 degree Celsius after a few days |
-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: Dec 14, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→59.9 Å / Num. obs: 51708 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 34.12 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.058 / Rrim(I) all: 0.151 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.5→2.57 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.803 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3691 / CC1/2: 0.796 / Rpim(I) all: 0.373 / Rrim(I) all: 0.954 / % possible all: 98.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4N7G Resolution: 2.5→59.9 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.905 / SU B: 19.831 / SU ML: 0.229 / Cross valid method: THROUGHOUT / ESU R: 0.38 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.368 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→59.9 Å
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Refine LS restraints |
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