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- PDB-7cxd: Xray structure of rat Galectin-3 CRD in complex with TD-139 belon... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7cxd | ||||||
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Title | Xray structure of rat Galectin-3 CRD in complex with TD-139 belonging to P121 space group | ||||||
![]() | Galectin-3 | ||||||
![]() | SUGAR BINDING PROTEIN / Beta-galactose binding protein / CARBOHYDRATE / TD-139 | ||||||
Function / homology | ![]() negative regulation of cell proliferation in bone marrow / advanced glycation end-product receptor activity / positive regulation of serotonin secretion / 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 / regulation of T cell apoptotic process / mononuclear cell migration / negative regulation of endocytosis / IgE binding ...negative regulation of cell proliferation in bone marrow / advanced glycation end-product receptor activity / positive regulation of serotonin secretion / 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 / regulation of T cell apoptotic process / mononuclear cell migration / negative regulation of endocytosis / IgE binding / positive regulation of mononuclear cell migration / Fc-gamma receptor I complex binding / eosinophil chemotaxis / regulation of extrinsic apoptotic signaling pathway via death domain receptors / monosaccharide binding / Neutrophil degranulation / 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 / glial cell projection / immunological synapse / laminin binding / epithelial cell differentiation / RNA splicing / extracellular matrix organization / neutrophil chemotaxis / extracellular matrix / skeletal system development / 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 / positive regulation of angiogenesis / protein phosphatase binding / mitochondrial inner membrane / external side of plasma membrane / innate immune response / positive regulation of cell population proliferation / negative regulation of apoptotic process / cell surface / extracellular space / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kumar, A. | ||||||
![]() | ![]() Title: Molecular mechanism of interspecies differences in the binding affinity of TD139 to Galectin-3. Authors: Kumar, A. / Paul, M. / Panda, M. / Jayaram, S. / Kalidindi, N. / Sale, H. / Vetrichelvan, M. / Gupta, A. / Mathur, A. / Beno, B. / Regueiro-Ren, A. / Cheng, D. / Ramarao, M. / Ghosh, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 135.2 KB | Display | ![]() |
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PDB format | ![]() | 104.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 26.6 KB | Display | |
Data in CIF | ![]() | 35.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7cxaSC ![]() 7cxbC ![]() 7cxcC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 16400.873 Da / Num. of mol.: 4 / Fragment: Carbohydrare Recognition Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-BR / #3: Chemical | ChemComp-TD2 / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.85 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 24-35% PEG 4000/6000, 0.1M Tris (pH 7.5 to pH 8.5), 0.1M MgCl2, 0.4M NaSCN |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 21, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.078 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.71→61.5 Å / Num. obs: 48235 / % possible obs: 87.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 27.23 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.045 / Rrim(I) all: 0.087 / Net I/σ(I): 9.3 / Num. measured all: 172697 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7CXA Resolution: 1.71→41.17 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.907 / SU R Cruickshank DPI: 0.164 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.163 / SU Rfree Blow DPI: 0.138 / SU Rfree Cruickshank DPI: 0.139
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Displacement parameters | Biso max: 97.06 Å2 / Biso mean: 31.73 Å2 / Biso min: 12.49 Å2
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Refine analyze | Luzzati coordinate error obs: 0.29 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.71→41.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.71→1.72 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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