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Carbohydrate anomalies in the PDB

Nature Chemical Biology volume 11, page 303 (2015)Cite this article

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An Erratum to this article was published on 17 June 2015

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To the Editor:

The importance of carbohydrates both to fundamental cellular biology and as integral parts of therapeutics (including antibodies) continues to grow. The presence of the correct glycans is important for the beneficial effects of therapeutic glycoproteins and is likely to be increasingly required by regulatory agencies. However, carbohydrates (and other small molecules) are handled poorly in macromolecular structural biology. When such small molecules are present in macromolecule structures, they are often reported with stereo- and regiochemical errors and in unlikely conformations. Stereo- and regiochemistry should always be correct, and although conformational distortions may reflect interactions taking place in a complex1, most are also likely to be erroneous—resulting from poor chemical understanding and lack of appropriate stereochemical restraints in refinement, often against low-resolution data2.

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Figure 1: Distribution of D-pyranoside ring conformations as a function of resolution for all N-linked sugars (at distance <2.0 Å) in the PDB as of January 2015, identified by their Chemical Component Dictionary IDs: NAG, NDG, MAN, BMA, BGC, GLC, GAL and GLA.

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Acknowledgements

This work was supported by Biotechnology and Biological Sciences Research Council grant BB/K008153/1.

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  1. Department of Chemistry, York Structural Biology Laboratory, The University of York, UK

    Jon Agirre, Gideon Davies, Keith Wilson & Kevin Cowtan

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  1. Jon Agirre
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  3. Keith Wilson
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  4. Kevin Cowtan
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Correspondence to Jon Agirre or Kevin Cowtan.

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Agirre, J., Davies, G., Wilson, K. et al. Carbohydrate anomalies in the PDB. Nat Chem Biol 11, 303 (2015). https://doi.org/10.1038/nchembio.1798

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