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Yorodumi- PDB-7cxc: Structure of mouse Galectin-3 CRD point mutant (V160A) in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7cxc | ||||||
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Title | Structure of mouse Galectin-3 CRD point mutant (V160A) in complex with TD-139 belonging to P121 space group. | ||||||
Components | Galectin-3 | ||||||
Keywords | SUGAR BINDING PROTEIN / beta-galactose binding protein / CARBOHYDRATE / TD-139 | ||||||
Function / homology | Function and homology information 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 / negative regulation of endocytosis / cornified envelope / IgE binding / Fc-gamma receptor I complex 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 / negative regulation of endocytosis / cornified envelope / IgE binding / Fc-gamma receptor I complex binding / eosinophil chemotaxis / monosaccharide binding / negative regulation of T cell receptor signaling pathway / positive chemotaxis / macrophage chemotaxis / positive regulation of calcium ion import / monocyte chemotaxis / glial cell projection / immunological synapse / laminin binding / neutrophil chemotaxis / Neutrophil degranulation / extracellular matrix / extracellular matrix organization / RNA splicing / skeletal system development / negative regulation of extrinsic apoptotic signaling pathway / spliceosomal complex / mRNA processing / positive regulation of angiogenesis / collagen-containing extracellular matrix / cell differentiation / external side of plasma membrane / innate immune response / positive regulation of cell population proliferation / negative regulation of apoptotic process / cell surface / extracellular space / extracellular region / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Kumar, A. | ||||||
Citation | Journal: Glycobiology / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cxc.cif.gz | 244 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cxc.ent.gz | 197.2 KB | Display | PDB format |
PDBx/mmJSON format | 7cxc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7cxc_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7cxc_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7cxc_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 7cxc_validation.cif.gz | 23.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cx/7cxc ftp://data.pdbj.org/pub/pdb/validation_reports/cx/7cxc | HTTPS FTP |
-Related structure data
Related structure data | 7cxaC 7cxbSC 7cxdC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18611.191 Da / Num. of mol.: 2 / Fragment: Carbohydrate Recognition Domain / Mutation: V160A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lgals3 / Production host: Escherichia coli (E. coli) / References: UniProt: P16110 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.84 Å3/Da / Density % sol: 33.16 % |
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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), 0.4M NaSCN |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12713 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Dec 17, 2016 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.12713 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.4→58.29 Å / Num. obs: 53247 / % possible obs: 77.7 % / Redundancy: 3.2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.029 / Rrim(I) all: 0.053 / Net I/σ(I): 16.9 / Num. measured all: 244146 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7CXB Resolution: 1.4→43.74 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.527 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.014 / ESU R Free: 0.013 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 92.31 Å2 / Biso mean: 14.564 Å2 / Biso min: 3.97 Å2
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Refinement step | Cycle: final / Resolution: 1.4→43.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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