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Yorodumi- PDB-7rdp: Crystal structure of human galectin-3 CRD in complex with selenod... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7rdp | ||||||
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Title | Crystal structure of human galectin-3 CRD in complex with selenodigalactoside | ||||||
Components | Galectin-3 | ||||||
Keywords | SUGAR BINDING PROTEIN / Galectin / carbohydrate-binding protein | ||||||
Function / homology | Function and homology information 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 / positive regulation of mononuclear cell migration / negative regulation of endocytosis / IgE binding ...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 / 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 / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | ||||||
Authors | Kishor, C. / Go, R.M. / Blanchard, H. | ||||||
Citation | Journal: Int J Mol Sci / Year: 2022 Title: Investigation of the Molecular Details of the Interactions of Selenoglycosides and Human Galectin-3. Authors: Raics, M. / Balogh, A.K. / Kishor, C. / Timari, I. / Medrano, F.J. / Romero, A. / Go, R.M. / Blanchard, H. / Szilagyi, L. / E Kover, K. / Feher, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7rdp.cif.gz | 47.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rdp.ent.gz | 29.7 KB | Display | PDB format |
PDBx/mmJSON format | 7rdp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rdp_validation.pdf.gz | 1003.4 KB | Display | wwPDB validaton report |
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Full document | 7rdp_full_validation.pdf.gz | 1003.3 KB | Display | |
Data in XML | 7rdp_validation.xml.gz | 8.1 KB | Display | |
Data in CIF | 7rdp_validation.cif.gz | 10.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rd/7rdp ftp://data.pdbj.org/pub/pdb/validation_reports/rd/7rdp | HTTPS FTP |
-Related structure data
Related structure data | 7rdoC 6b8kS 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: 15758.100 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 | ChemComp-4IZ / |
#3: Chemical | ChemComp-CL / |
#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: 2.13 Å3/Da / Density % sol: 42.25 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 31% PEG 3100, 100 mM tris-HCl pH 7.5, 100 mM MgCl2, 8 mM 2-Mercaptoethanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9737 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9737 Å / Relative weight: 1 |
Reflection | Resolution: 1.959→30.862 Å / Num. obs: 9287 / % possible obs: 91.3 % / Redundancy: 4.2 % / CC1/2: 0.999 / Net I/σ(I): 20.54 |
Reflection shell | Resolution: 1.96→2.03 Å / Mean I/σ(I) obs: 5.45 / Num. unique obs: 833 / CC1/2: 0.944 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6B8K Resolution: 1.96→30.86 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.13 / SU ML: 0.089 / Cross valid method: FREE R-VALUE / ESU R: 0.174 / ESU R Free: 0.141 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: 17.161 Å2
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Refinement step | Cycle: LAST / Resolution: 1.96→30.86 Å
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Refine LS restraints |
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LS refinement shell |
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