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Yorodumi- PDB-8aai: Crystal structure of the PDZ tandem of syntenin in complex with f... -
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-Basic information
Entry | Database: PDB / ID: 8aai | ||||||
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Title | Crystal structure of the PDZ tandem of syntenin in complex with fragment E5 | ||||||
Components | Syntenin-1 | ||||||
Keywords | SIGNALING PROTEIN / signaling protein cell adhesion PDZ domain syntenin syndecan drug design | ||||||
Function / homology | Function and homology information interleukin-5 receptor complex / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / syndecan binding / neurexin family protein binding / Neurofascin interactions / presynapse assembly / cytoskeletal anchor activity / substrate-dependent cell migration, cell extension / positive regulation of exosomal secretion ...interleukin-5 receptor complex / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / syndecan binding / neurexin family protein binding / Neurofascin interactions / presynapse assembly / cytoskeletal anchor activity / substrate-dependent cell migration, cell extension / positive regulation of exosomal secretion / frizzled binding / negative regulation of receptor internalization / protein targeting to membrane / Ephrin signaling / RIPK1-mediated regulated necrosis / positive regulation of transforming growth factor beta receptor signaling pathway / growth factor binding / positive regulation of epithelial to mesenchymal transition / positive regulation of phosphorylation / cell adhesion molecule binding / protein sequestering activity / regulation of mitotic cell cycle / phosphatidylinositol-4,5-bisphosphate binding / ephrin receptor binding / adherens junction / positive regulation of JNK cascade / ionotropic glutamate receptor binding / Regulation of necroptotic cell death / azurophil granule lumen / extracellular vesicle / melanosome / presynapse / actin cytoskeleton organization / positive regulation of cell growth / chemical synaptic transmission / nuclear membrane / Ras protein signal transduction / blood microparticle / cytoskeleton / intracellular signal transduction / positive regulation of cell migration / protein heterodimerization activity / membrane raft / focal adhesion / positive regulation of cell population proliferation / Neutrophil degranulation / endoplasmic reticulum membrane / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å | ||||||
Authors | Feracci, M. / Barral, K. | ||||||
Funding support | France, 1items
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Citation | Journal: J.Med.Chem. / Year: 2023 Title: Discovery of a PDZ Domain Inhibitor Targeting the Syndecan/Syntenin Protein-Protein Interaction: A Semi-Automated "Hit Identification-to-Optimization" Approach. Authors: Hoffer, L. / Garcia, M. / Leblanc, R. / Feracci, M. / Betzi, S. / Ben Yaala, K. / Daulat, A.M. / Zimmermann, P. / Roche, P. / Barral, K. / Morelli, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8aai.cif.gz | 261.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8aai.ent.gz | 206.5 KB | Display | PDB format |
PDBx/mmJSON format | 8aai.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aa/8aai ftp://data.pdbj.org/pub/pdb/validation_reports/aa/8aai | HTTPS FTP |
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-Related structure data
Related structure data | 8aakC 8aaoC 8aapC 1n99S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 1 / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 111 - 272 / Label seq-ID: 4 - 165
NCS ensembles :
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-Components
#1: Protein | Mass: 18018.688 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SDCBP, MDA9, SYCL / Production host: Escherichia coli (E. coli) / References: UniProt: O00560 #2: Chemical | ChemComp-LKV / ( #3: Water | ChemComp-HOH / | 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: 2.25 Å3/Da / Density % sol: 45.23 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop Details: 100mM Sodium Acetate 200mM Ammonium acetate 20% PEG 3350 PH range: 4.4 - 4.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 19, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.76→27.63 Å / Num. obs: 15909 / % possible obs: 97.29 % / Redundancy: 5.27 % / Rmerge(I) obs: 0.1388 / Rpim(I) all: 0.08908 / Net I/σ(I): 5.27 |
Reflection shell | Resolution: 2.76→2.859 Å / Rmerge(I) obs: 0.4417 / Mean I/σ(I) obs: 2.26 / Num. unique obs: 1613 / Rpim(I) all: 0.288 / % possible all: 96.74 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1N99 Resolution: 2.76→27.63 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.871 / SU B: 26.151 / SU ML: 0.507 / Cross valid method: FREE R-VALUE / ESU R Free: 0.528 Details: Hydrogens have been added in their 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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.548 Å2
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Refinement step | Cycle: LAST / Resolution: 2.76→27.63 Å
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Refine LS restraints |
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