Abstract
Knowledge of the three-dimensional structures of the carbohydrate molecules is indispensable for a full understanding of the molecular processes in which carbohydrates are involved, such as protein glycosylation or protein-carbohydrate interactions. The Protein Data Bank (PDB) is a valuable resource for three-dimensional structural information on glycoproteins and protein-carbohydrate complexes. Unfortunately, many carbohydrate moieties in the PDB contain inconsistencies or errors. This article gives an overview of the information that can be obtained from individual PDB entries and from statistical analyses of sets of three-dimensional structures, of typical problems that arise during the analysis of carbohydrate three-dimensional structures and of the validation tools that are currently available to scientists to evaluate the quality of these structures.
Highlights
To sion whether a mismatch is caused by a wrong residue name or judge the quality of the observed torsions, comparison data erroneous coordinates cannot be made without further are needed. These can be retrieved from the carbohydrate knowledge of the experimental conditions
With more than 3500 entries for glycoproteins or protein– carbohydrate complexes, the Protein Data Bank (PDB) forms a valuable resource for glycoscientists
Many errors and problems occur within the carbohydrate moieties of these PDB entries
Summary
Carbohydrates, often referred to as glycans, play an important role in many biological and biochemical processes, ranging from protein folding to a variety of recognition events, many of which are of immunological importance (Varki et al, 1999; Helenius & Aebi, 2001; Ohtsubo & Marth, 2006). The developmental age and the health/disease state of a cell, different glycosyltransferases, the enzymes that build the glycans in a non-template-driven fashion, are expressed (Kornfeld & Kornfeld, 1985; Schachter, 2000; Esko & Selleck, 2002; Ohtsubo & Marth, 2006). This results in different primary structures of the glycans and allows a ‘fine-tuning’ of proteins (Helenius & Aebi, 2001; Drescher et al, 2003). The GPI-anchored protein CD59, for example, consists of a heterogeneous mixture of more than 120 glycoforms (Rudd et al, 1997)
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