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- PDB-6y8d: 14-3-3 Sigma in complex with phosphorylated caspase{pS164} peptide -
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Open data
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Basic information
Entry | Database: PDB / ID: 6y8d | ||||||
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Title | 14-3-3 Sigma in complex with phosphorylated caspase{pS164} peptide | ||||||
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![]() | PROTEIN BINDING / 14-3-3 / caspase{pS164} / complex / protein / protein-protein interactions | ||||||
Function / homology | ![]() caspase-2 / endopeptidase complex / neural retina development / NADE modulates death signalling / luteolysis / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / cysteine-type endopeptidase activity involved in execution phase of apoptosis / execution phase of apoptosis / regulation of epidermal cell division / protein kinase C inhibitor activity ...caspase-2 / endopeptidase complex / neural retina development / NADE modulates death signalling / luteolysis / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / cysteine-type endopeptidase activity involved in execution phase of apoptosis / execution phase of apoptosis / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / TP53 Regulates Transcription of Caspase Activators and Caspases / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / ectopic germ cell programmed cell death / 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 / extrinsic apoptotic signaling pathway in absence of ligand / RHO GTPases activate PKNs / protein sequestering activity / protein kinase A signaling / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / 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 / positive regulation of apoptotic signaling pathway / positive regulation of protein export from nucleus / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / apoptotic signaling pathway / negative regulation of protein kinase activity / NOD1/2 Signaling Pathway / protein processing / cellular response to mechanical stimulus / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of neuron apoptotic process / protein localization / positive regulation of cell growth / regulation of cell cycle / cadherin binding / positive regulation of apoptotic process / protein domain specific binding / cysteine-type endopeptidase activity / DNA damage response / nucleolus / negative regulation of apoptotic process / apoptotic process / protein kinase binding / negative regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / extracellular space / extracellular exosome / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ballone, A. / Lau, R.A. / Zweipfenning, F.P.A. / Ottmann, C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A new soaking procedure for X-ray crystallographic structural determination of protein-peptide complexes. Authors: Ballone, A. / Lau, R.A. / Zweipfenning, F.P.A. / 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 | ![]() | 87.6 KB | Display | ![]() |
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PDB format | ![]() | 52.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6y3mC ![]() 6y3oC ![]() 6y3rC ![]() 6y3sC ![]() 6y3vC ![]() 6y40C ![]() 6y44C ![]() 6y8aC ![]() 6y8bC ![]() 6y8eC ![]() 3lw1S 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 on special symmetry positions |
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Components
#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: 1022.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() | ||||||
#3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.38 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 28% PEG400, 5% glycerol, 0.2M CaCl, 0.1M HEPES pH 7.5, 2mM BME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 28, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.973 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→29.41 Å / Num. obs: 45100 / % possible obs: 97.6 % / Redundancy: 11.4 % / Biso Wilson estimate: 15.38 Å2 / CC1/2: 1 / Net I/σ(I): 64.3 |
Reflection shell | Resolution: 1.51→1.54 Å / Num. unique obs: 1757 / CC1/2: 0.986 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3lw1 Resolution: 1.51→29.41 Å / SU ML: 0.1182 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.1446
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.06 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.51→29.41 Å
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Refine LS restraints |
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LS refinement shell |
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