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Yorodumi- PDB-7df5: Human Galectin-3 CRD in complex with novel tetrahydropyran-based ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7df5 | ||||||
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Title | Human Galectin-3 CRD in complex with novel tetrahydropyran-based thiodisaccharide mimic inhibitor | ||||||
Components | Galectin-3 | ||||||
Keywords | CARBOHYDRATE / Inhibitor / Complex / Galectin-3 CRD | ||||||
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 / negative regulation of endocytosis / IgE binding / 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 / negative regulation of endocytosis / IgE binding / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å | ||||||
Authors | Ghosh, K. / Kumar, A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2021 Title: Synthesis, Structure-Activity Relationships, and In Vivo Evaluation of Novel Tetrahydropyran-Based Thiodisaccharide Mimics as Galectin-3 Inhibitors. Authors: Xu, L. / Hartz, R.A. / Beno, B.R. / Ghosh, K. / Shukla, J.K. / Kumar, A. / Patel, D. / Kalidindi, N. / Lemos, N. / Gautam, S.S. / Kumar, A. / Ellsworth, B.A. / Shah, D. / Sale, H. / Cheng, D. / Regueiro-Ren, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7df5.cif.gz | 136.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7df5.ent.gz | 104.7 KB | Display | PDB format |
PDBx/mmJSON format | 7df5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7df5_validation.pdf.gz | 733.7 KB | Display | wwPDB validaton report |
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Full document | 7df5_full_validation.pdf.gz | 735.3 KB | Display | |
Data in XML | 7df5_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 7df5_validation.cif.gz | 14.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/7df5 ftp://data.pdbj.org/pub/pdb/validation_reports/df/7df5 | HTTPS FTP |
-Related structure data
Related structure data | 7df6C 7cxaS 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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Unit cell |
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-Components
#1: Protein | Mass: 18565.160 Da / Num. of mol.: 1 / Fragment: Carbohydrate Recoginition Domain (CRD) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS3, MAC2 / Production host: Escherichia coli (E. coli) / References: UniProt: P17931 | ||||||
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#2: Chemical | ChemComp-MG / | ||||||
#3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-H5O / ( | #5: 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: 1.74 Å3/Da / Density % sol: 29.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1M Tris (pH 7.5-8.5), 0.1M MgCl2, 0.4M NaSCN, 28-35% PEG 4000 or PEG 6000 PH range: 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.969 Å | ||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Jul 30, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.969 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.08→42.12 Å / Num. obs: 56223 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.02 / Rrim(I) all: 0.054 / Net I/σ(I): 18 / Num. measured all: 390205 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7CXA Resolution: 1.08→31.3 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.897 / SU ML: 0.019 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.028 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 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: 75.07 Å2 / Biso mean: 14.735 Å2 / Biso min: 8.31 Å2
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Refinement step | Cycle: final / Resolution: 1.08→31.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.08→1.108 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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