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Open data
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Basic information
Entry | Database: PDB / ID: 5h9r | ||||||||||||
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Title | Crystal Structure of Human Galectin-3 CRD in Complex with TAZTDG | ||||||||||||
![]() | Galectin-3 | ||||||||||||
![]() | SUGAR BINDING PROTEIN / galectin / thio-digalactoside (TDG) / pi-arginine interaction / fluorine bonding | ||||||||||||
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 / 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 / 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 / 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 / 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 | ![]() ![]() ![]() | ||||||||||||
![]() | Hsieh, T.J. / Lin, H.Y. / Lin, C.H. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Dual thio-digalactoside-binding modes of human galectins as the structural basis for the design of potent and selective inhibitors Authors: Hsieh, T.J. / Lin, H.Y. / Tu, Z. / Lin, T.C. / Wu, S.C. / Tseng, Y.Y. / Liu, F.T. / Danny Hsu, S.T. / Lin, C.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 | ![]() | 48.8 KB | Display | ![]() |
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PDB format | ![]() | 31.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 725.6 KB | Display | ![]() |
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Full document | ![]() | 725.6 KB | Display | |
Data in XML | ![]() | 9 KB | Display | |
Data in CIF | ![]() | 12.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4y24C ![]() 5h9pC ![]() 5h9qC ![]() 5h9sC ![]() 2nmnS 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: 17872.418 Da / Num. of mol.: 1 Fragment: carbohydrate-recognition domain, UNP residues 113-250 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: P17931 |
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#2: Chemical | ChemComp-TGZ / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34.26 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris pH8.5, 0.2 M MgCl2, 30% (w/v) PEG 3350 / PH range: 7.5-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 2, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97622 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→30 Å / Num. obs: 18965 / % possible obs: 99.7 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 1.58→1.64 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 3.32 / % possible all: 98.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2NMN Resolution: 1.58→26.225 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.03 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.58→26.225 Å
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Refine LS restraints |
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LS refinement shell |
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