+Open data
-Basic information
Entry | Database: PDB / ID: 5nfa | |||||||||
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Title | Structure of Galectin-3 CRD in complex with compound 3 | |||||||||
Components | Galectin-3 | |||||||||
Keywords | SUGAR BINDING PROTEIN / Galectin-3 CRD / cation-Pi interactions | |||||||||
Function / homology | Function and homology information negative regulation of protein tyrosine phosphatase activity / negative regulation of immunological synapse formation / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / RUNX2 regulates genes involved in differentiation of myeloid cells / disaccharide binding / regulation of T cell apoptotic process / mononuclear cell migration / IgE binding / negative regulation of endocytosis / positive regulation of mononuclear cell migration ...negative regulation of protein tyrosine phosphatase activity / negative regulation of immunological synapse formation / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / RUNX2 regulates genes involved in differentiation of myeloid cells / disaccharide binding / regulation of T cell apoptotic process / mononuclear cell migration / IgE binding / negative regulation of endocytosis / positive regulation of mononuclear cell migration / eosinophil chemotaxis / regulation of extrinsic apoptotic signaling pathway via death domain receptors / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / protein phosphatase inhibitor activity / negative regulation of T cell receptor signaling pathway / positive chemotaxis / regulation of T cell proliferation / positive regulation of calcium ion import / macrophage chemotaxis / chemoattractant activity / monocyte chemotaxis / Advanced glycosylation endproduct receptor signaling / ficolin-1-rich granule membrane / immunological synapse / laminin binding / epithelial cell differentiation / neutrophil chemotaxis / RNA splicing / secretory granule membrane / molecular condensate scaffold activity / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein localization to plasma membrane / spliceosomal complex / positive regulation of protein-containing complex assembly / mRNA processing / carbohydrate binding / protein phosphatase binding / collagen-containing extracellular matrix / mitochondrial inner membrane / innate immune response / Neutrophil degranulation / cell surface / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å | |||||||||
Authors | Ronin, C. / Atmanene, C. / Gautier, F.M. / Djedaini Pilard, F. / Teletchea, S. / Ciesielski, F. / Vivat Hannah, V. / Grandjean, C. | |||||||||
Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2017 Title: Biophysical and structural characterization of mono/di-arylated lactosamine derivatives interaction with human galectin-3. Authors: Atmanene, C. / Ronin, C. / Teletchea, S. / Gautier, F.M. / Djedaini-Pilard, F. / Ciesielski, F. / Vivat, V. / Grandjean, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nfa.cif.gz | 50.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nfa.ent.gz | 33.6 KB | Display | PDB format |
PDBx/mmJSON format | 5nfa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nf/5nfa ftp://data.pdbj.org/pub/pdb/validation_reports/nf/5nfa | HTTPS FTP |
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-Related structure data
Related structure data | 5nf7C 5nf9C 5nfbC 5nfcC 3zslS C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 16458.844 Da / Num. of mol.: 1 / Fragment: UNP residues 106-250 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS3, MAC2 / Production host: Escherichia coli (E. coli) / References: UniProt: P17931 |
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#2: Polysaccharide | 3-O-[(3-methoxyphenyl)methyl]-beta-D-galactopyranose-(1-4)-N-acetyl-2-(acetylamino)-2-deoxy-beta-D- ...3-O-[(3-methoxyphenyl)methyl]-beta-D-galactopyranose-(1-4)-N-acetyl-2-(acetylamino)-2-deoxy-beta-D-glucopyranosylamine Type: oligosaccharide / Mass: 544.549 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 27.33 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100mM Tris HCl pH7.5; 30-34% PEG4000; 100mM MgCl2; 400mM NaSCN; 8mM beta-mercaptoethanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 27, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→50 Å / Num. obs: 18804 / % possible obs: 99.2 % / Redundancy: 6.1 % / Rsym value: 0.038 / Net I/σ(I): 28.3 |
Reflection shell | Resolution: 1.59→1.68 Å / Rsym value: 0.128 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3zsl Resolution: 1.59→42.75 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.253 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.076 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.869 Å2
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Refinement step | Cycle: 1 / Resolution: 1.59→42.75 Å
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