GAG-DB

GAG-DB provides a curated three-dimensional repository of the six mammalian glycosaminoglycans—chondroitin sulfate, dermatan sulfate, heparin, heparan sulfate, hyaluronan, and keratan sulfate—and their oligosaccharide complexes bound to proteins for analysis of structures and protein–GAG interactions.

Key Features:

• Three-Dimensional Structural Data: Contains GAG and GAG–protein complex structures determined by X-ray single-crystal diffraction, X-ray fiber diffractometry, solution NMR spectroscopy, scattering data, and molecular modeling.
• Integration with Major Bioinformatics Resources: Enables queries and cross-referencing using identifiers from the Protein Data Bank (PDB), UniProtKB, and GlyTouCan.
• Graphical and Numerical Representation: Provides graphical depictions of bound glycan ligands and numerical formats for detailed analysis and cross-referencing to other glycoscience databases and functional datasets.
• Interaction Analysis: Reports interactions between GAGs and protein ligands and evaluates binding at monosaccharide and quaternary-structure levels.

Scientific Applications:

• Structural characterization: Support studies of the molecular architecture of GAGs and their oligosaccharide conformations.
• Protein–GAG interaction analysis: Enable investigation of binding sites, contact residues, and binding modes between proteins and GAGs.
• Functional inference: Aid understanding of the structural basis for GAG roles in physiological and pathological processes.

Methodology:

Molecular modeling and computational evaluation of binding interactions at monosaccharide and quaternary-structure levels, used alongside scattering data and experimental structural determinations.