Carbohydrate 3D structure validation

Abstract

Glycoproteins and protein-carbohydrate complexes in the worldwide Protein Data Bank (wwPDB) can be an excellent source of information for glycoscientists. Unfortunately, a rather large number of errors and inconsistencies is found in the glycan moieties of these 3D structures. This review illustrates frequent problems of carbohydrate moieties in wwPDB entries, such as nomenclature issues, incorrect N-glycan core structures, missing or erroneous linkages, or poor glycan geometry, and describes the carbohydrate-specific validation tools that are designed to identify such problems. Recommendations how to avoid these issues or how to rectify incorrect structures are also given.