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Yorodumi- PDB-7az2: 14-3-3 sigma with Pin1 binding site pS72 and covalently bound LvD1014 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7az2 | |||||||||
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Title | 14-3-3 sigma with Pin1 binding site pS72 and covalently bound LvD1014 | |||||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / 1433 / Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 | |||||||||
Function / homology | Function and homology information 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 / postsynaptic cytosol / mitogen-activated protein kinase kinase binding / regulation of mitotic nuclear division / 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 / postsynaptic cytosol / mitogen-activated protein kinase kinase binding / regulation of mitotic nuclear division / 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 / 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 / protein peptidyl-prolyl isomerization / 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 protein dephosphorylation / RHO GTPases activate PKNs / protein kinase A signaling / protein sequestering activity / 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 / ciliary basal body / positive regulation of GTPase activity / regulation of cytokinesis / negative regulation of protein binding / stem cell proliferation / 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 / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / tau protein binding / neuron differentiation / negative regulation of protein catabolic process / negative regulation of ERK1 and ERK2 cascade / ISG15 antiviral mechanism / beta-catenin binding / intrinsic apoptotic signaling pathway in response to DNA damage / 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 / protein stabilization / response to hypoxia / regulation of cell cycle / nuclear speck / cadherin binding / positive regulation of protein phosphorylation / cell cycle / 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 / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.081 Å | |||||||||
Authors | Wolter, M. / Dijck, L.v. / Ottmann, C. | |||||||||
Funding support | 2items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7az2.cif.gz | 76.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7az2.ent.gz | 53.6 KB | Display | PDB format |
PDBx/mmJSON format | 7az2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7az2_validation.pdf.gz | 673.7 KB | Display | wwPDB validaton report |
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Full document | 7az2_full_validation.pdf.gz | 674.5 KB | Display | |
Data in XML | 7az2_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 7az2_validation.cif.gz | 22.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/7az2 ftp://data.pdbj.org/pub/pdb/validation_reports/az/7az2 | HTTPS FTP |
-Related structure data
Related structure data | 7aogSC 7axnC 7ayfC 7az1C 7bdpC 7bdtC 7bdyC 7bfwC 7bg3C 7bgqC 7bgrC 7bgvC 7bgwC 7nifC 7nigC 7nixC 7nj6C 7nj8C 7njaC 7nqpC 7nrkC 7nrlC 7nsvC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: 28169.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31947 |
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#2: Protein/peptide | Mass: 2195.378 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13526, peptidylprolyl isomerase |
-Non-polymers , 4 types, 356 molecules
#3: Chemical | ChemComp-SFW / | ||||
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#4: Chemical | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.75 % |
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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: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97627 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97627 Å / Relative weight: 1 |
Reflection | Resolution: 1.08→66.242 Å / Num. obs: 119445 / % possible obs: 97.4 % / Redundancy: 1.9 % / Biso Wilson estimate: 13.95 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.027 / Rrim(I) all: 0.039 / Rsym value: 0.027 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.08→1.1 Å / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4601 / CC1/2: 0.425 / Rpim(I) all: 0.684 / Rrim(I) all: 0.967 / % possible all: 76.9 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7AOG Resolution: 1.081→66.242 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.46 / 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: 76.18 Å2 / Biso mean: 21.3611 Å2 / Biso min: 10.57 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.081→66.242 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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