A clearer 3D view of sugars

glycosylation shown in 3D-SNFG, ball-and-stick and combined
12 October 2017

Carbohydrates, even when formed from very few sugar units, can often be hard to interpret in three dimensions when all their atoms are shown. This week, we have updated the 3D structure viewer on our web pages to add a simpler representation of common pyranose sugars.

LiteMol, created by CEITEC (Brno, Czech Republic) and PDBe, now supports the 3D-Symbol Nomenclature For Glycans (3D-SNFG) representation. 3D-SNFG uses 3D versions of the 2D geometric shapes commonly accepted to denote sugars in the glycobiology community. Placing coloured shapes in the centre of the sugar ring greatly simplifies the view of sugars, in the same way that the cartoon representation does for proteins and nucleic acids.

The image to the left shows the sugars decorating human parasite invasion inhibitory antibody (PDB entry 5ezi). The 3D-SNFG representation (middle panel) makes identifying the types of sugars and how they are connected much easier when compared to the ball-and-stick view (top panel). Both types of representation can also be shown at once (lower panel). The same structure is shown in 3D in LiteMol below. The ‘Carbohydrate 3D symbol’ part of the LiteMol menu is used to control the display of these symbols.

Approximately 10% of entries in the PDB archive contain some form of carbohydrate - that’s around 13.5 thousand PDB entries! We hope that adding this new feature will help users to see them more clearly.