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- PDB-4jc1: Galectin-3 carbohydrate recognition domain in complex with thiodi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4jc1 | ||||||||||||
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Title | Galectin-3 carbohydrate recognition domain in complex with thiodigalactoside | ||||||||||||
![]() | Galectin-3 | ||||||||||||
![]() | SUGAR BINDING PROTEIN / beta sandwich / carbohydrate binding protein | ||||||||||||
Function / homology | ![]() negative regulation of protein tyrosine phosphatase activity / negative regulation of immunological synapse formation / disaccharide binding / 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 / regulation of T cell apoptotic process / mononuclear cell migration / positive regulation of mononuclear cell migration / negative regulation of endocytosis / IgE binding ...negative regulation of protein tyrosine phosphatase activity / negative regulation of immunological synapse formation / disaccharide binding / 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 / regulation of T cell apoptotic process / mononuclear cell migration / positive regulation of mononuclear cell migration / negative regulation of endocytosis / IgE binding / 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 / regulation of T cell proliferation / positive chemotaxis / positive regulation of calcium ion import / chemoattractant activity / macrophage chemotaxis / monocyte chemotaxis / Advanced glycosylation endproduct receptor signaling / ficolin-1-rich granule membrane / immunological synapse / laminin binding / epithelial cell differentiation / RNA splicing / neutrophil chemotaxis / 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 / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() | ||||||||||||
![]() | Collins, P.M. / Blanchard, H. | ||||||||||||
![]() | ![]() Title: Investigation into the feasibility of thioditaloside as a novel scaffold for galectin-3-specific inhibitors. Authors: Bum-Erdene, K. / Gagarinov, I.A. / Collins, P.M. / Winger, M. / Pearson, A.G. / Wilson, J.C. / Leffler, H. / Nilsson, U.J. / Grice, I.D. / Blanchard, H. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 83.7 KB | Display | ![]() |
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PDB format | ![]() | 60.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 750.7 KB | Display | ![]() |
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Full document | ![]() | 751.9 KB | Display | |
Data in XML | ![]() | 9.4 KB | Display | |
Data in CIF | ![]() | 12.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4jckC ![]() 1a3kS C: citing same article ( 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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Unit cell |
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Components
#1: Protein | Mass: 16054.424 Da / Num. of mol.: 1 / Fragment: galectin-3: unp residues 108-250 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Polysaccharide | beta-D-galactopyranose-(1-1)-1-thio-beta-D-galactopyranose![]() Source method: isolated from a genetically manipulated source Details: oligosaccharide with S-glycosidic bond between monosaccharides, and with reducing-end-to-reducing-end glycosidic bond References: thiodigalactoside | ||
#3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Hanging drops consisting of equal volumes of protein solution (100 mM lactose in PBS pH 7.5 supplemented with 2 mM CaCl2 and a protein concentration of 10 mg ml 1) and reservoir solution ...Details: Hanging drops consisting of equal volumes of protein solution (100 mM lactose in PBS pH 7.5 supplemented with 2 mM CaCl2 and a protein concentration of 10 mg ml 1) and reservoir solution [100 mM Tris HCl, 31%(w/v) PEG 6000, 100 mM MgCl2 and 8 mM -mercaptoethanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ![]() |
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: Jun 23, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→58 Å / Num. all: 115029 / Num. obs: 21329 / % possible obs: 95.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.142 / Mean I/σ(I) obs: 3.5 / % possible all: 84.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1A3K Resolution: 1.5→42.79 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.971 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.091 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Solvent model: BABINET MODEL PARAMETERS FOR MASK CACLULATION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.799 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→42.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 13.1631 Å / Origin y: 0.6809 Å / Origin z: 6.5799 Å
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