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- PDB-7rh3: Co-crystallization of human galectin-3 CRD complex with Methyl 2-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7rh3 | ||||||
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Title | Co-crystallization of human galectin-3 CRD complex with Methyl 2-O-(2-nitro-4-chloro)-benzoyl-3-O-toluoyl-b-D-talopyranoside | ||||||
![]() | Galectin-3 | ||||||
![]() | SUGAR BINDING PROTEIN / Carbohydrates-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 / 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 | ![]() ![]() ![]() | ||||||
![]() | Collins, P.M. / Kishor, C. / Blanchard, H. | ||||||
![]() | ![]() Title: Novel Selective Galectin-3 Antagonists Are Cytotoxic to Acute Lymphoblastic Leukemia. Authors: Bum-Erdene, K. / Collins, P.M. / Hugo, M.W. / Tarighat, S.S. / Fei, F. / Kishor, C. / Leffler, H. / Nilsson, U.J. / Groffen, J. / Grice, I.D. / Heisterkamp, N. / 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 | ![]() | 53.6 KB | Display | ![]() |
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PDB format | ![]() | 33.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 804.4 KB | Display | ![]() |
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Full document | ![]() | 805.4 KB | Display | |
Data in XML | ![]() | 10.3 KB | Display | |
Data in CIF | ![]() | 14.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7rgxC ![]() 7rgyC ![]() 7rgzC ![]() 7rh0C ![]() 7rh1C ![]() 7rh4C ![]() 2nmoS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 15735.129 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-59O / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100 mM Tris-HCl, pH 7.0, 100 mM MgCl2, 31-35 % w/v polyethylene glycol 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 15, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.05→31.27 Å / Num. obs: 61577 / % possible obs: 99.9 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 24.1 |
Reflection shell | Resolution: 1.05→1.07 Å / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 2975 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2NMO Resolution: 1.05→30.701 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.361 / SU ML: 0.019 / Cross valid method: FREE R-VALUE / ESU R: 0.028 / ESU R Free: 0.029 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: 8.985 Å2
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Refinement step | Cycle: LAST / Resolution: 1.05→30.701 Å
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Refine LS restraints |
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LS refinement shell |
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