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Yorodumi- PDB-7rh0: Crystal structure of human galectin-3 CRD in complex with Methyl ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7rh0 | ||||||
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Title | Crystal structure of human galectin-3 CRD in complex with Methyl 2-O-(2-nitro-4-trifluoromethyl-benzoyl)-3-O-toluoyl-b-D-talopyranoside | ||||||
Components | Galectin-3 | ||||||
Keywords | SUGAR BINDING PROTEIN / Carbohydrates-binding protein | ||||||
Function / homology | Function and homology information : / 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 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 / macrophage chemotaxis / positive regulation of calcium ion import / chemoattractant activity / monocyte chemotaxis / Advanced glycosylation endproduct receptor signaling / ficolin-1-rich granule membrane / immunological synapse / epithelial cell differentiation / laminin binding / neutrophil chemotaxis / positive regulation of protein localization to plasma membrane / RNA splicing / secretory granule membrane / molecular condensate scaffold activity / negative regulation of extrinsic apoptotic signaling pathway / spliceosomal complex / positive regulation of protein-containing complex assembly / mRNA processing / protein phosphatase binding / carbohydrate 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.487 Å | ||||||
Authors | Collins, P.M. / Kishor, C. / Blanchard, H. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7rh0.cif.gz | 51.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rh0.ent.gz | 32.4 KB | Display | PDB format |
PDBx/mmJSON format | 7rh0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rh0_validation.pdf.gz | 769 KB | Display | wwPDB validaton report |
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Full document | 7rh0_full_validation.pdf.gz | 769 KB | Display | |
Data in XML | 7rh0_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | 7rh0_validation.cif.gz | 13.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rh/7rh0 ftp://data.pdbj.org/pub/pdb/validation_reports/rh/7rh0 | HTTPS FTP |
-Related structure data
Related structure data | 7rgxC 7rgyC 7rgzC 7rh1C 7rh3C 7rh4C 2nmoS 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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1 |
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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.) Homo sapiens (human) / Gene: LGALS3, MAC2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P17931 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-5BI / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 31% PEG 6000, 100mM MgCl2, 8mM beta mercaptoethanol, 100mM Tris-HCL, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 9, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.487→42.433 Å / Num. obs: 19606 / % possible obs: 88.3 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.49→1.51 Å / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 184 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2NMO Resolution: 1.487→42.433 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.056 / SU ML: 0.073 / Cross valid method: FREE R-VALUE / ESU R: 0.095 / ESU R Free: 0.101 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: 17.809 Å2
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Refinement step | Cycle: LAST / Resolution: 1.487→42.433 Å
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Refine LS restraints |
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LS refinement shell |
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