Carbohydrates
are well known for their physicochemical, biological,
functional, and therapeutic characteristics. Unfortunately, their
chemical nature imposes severe challenges for the structural elucidation
of these phenomena, impairing not only the depth of our understanding
of carbohydrates but also the development of new biotechnological
and therapeutic applications based on these molecules. In the recent
past, the amount of structural information, obtained mainly from X-ray
crystallography, has increased progressively, as well as its quality.
In this context, the current work presents a global analysis of the
carbohydrate information available in the Protein Data Bank (PDB).
From high quality structures, it is clear that most of the data are
highly concentrated on a few sets of residue types, on their monosaccharidic
forms, and connected by a small diversity of glycosidic linkages.
The geometries of these linkages can be mostly associated with the
types of linkages instead of residues, while the level of puckering
distortion was characterized, quantified, and located in a pseudorotational
equilibrium landscape, not only to local minima but also to transitional
states. These qualitative and quantitative analyses offer a global
picture of the carbohydrate structural content in the PDB, potentially
supporting the building of new models for carbohydrate-related biological
phenomena at the atomistic level, including new developments on force
field parameters.
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