Carbohydrate 3D structure validation.
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.
Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
Robbie P
RP
Joosten
Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Frankfurter Str. 100, 35392 Giessen, Germany. Electronic address: thomas.luetteke@vetmed.uni-giessen.de.
Thomas
T
Lütteke
D000818:Animals; D002241:Carbohydrates / Q000737:chemistry*; D030562:Databases, Protein; D006801:Humans; D011134:Polysaccharides / Q000737:chemistry; D015203:Reproducibility of Results
D002241:Carbohydrates; D011134:Polysaccharides