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Privateer: software for the conformational validation of carbohydrate structures

Nature Structural & Molecular Biology volume 22, pages 833–834 (2015)Cite this article

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Privateer (http://www.ccp4.ac.uk/html/privateer.html) is a new software package aimed at the detection and prevention of conformational, regiochemical and stereochemical anomalies in cyclic monosaccharide structures.

Carbohydrates, including O- and N-glycans attached to protein and lipid structures, are increasingly being studied in cellular biology. Crystallographic refinement of sugars is, however, poorly performed, thus leading to thousands of incorrect structures having been deposited in the Protein Data Bank (PDB)1,2. Although nomenclature validation has become possible in the past decade, with the introduction of tools such as PDB carbohydrate residue check (pdb-care)3, inappropriate refinement protocols at resolutions lower than 1.6 Å can still force a correct sugar into a highly improbable ring conformation, let alone distort one with chemical errors1. High-energy conformations are very infrequent in nature—perhaps even out of the question in N-glycans—and must always be backed by clear electron density. Otherwise, such conformations should be treated as outliers.

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Figure 1: N-glycan D-pyranosides in high-energy conformations, as deposited in the PDB (left), and their corrected counterparts (right).

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Acknowledgements

This work was supported by the Biotechnology and Biological Sciences Research Council grant BB/K008153/1 (to K.S.W. and K.D.C.), Ministerio de Economía y Competitividad (MINECO) grant CTQ2014-55174-P (to C.R.) and Agència de Gestió d'Ajuts Universitaris i de Recerca (AGAUR) grant 2014SGR-987 (to C.R.). The authors thank E. Krissinel (CCP4) for valuable assistance in using CCP4SRS and the Barcelona Supercomputing Center (BSC) for providing computing support.

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  1. Javier Iglesias-Fernández

    Present address: Present address: Department of Chemistry, King's College, London, UK.,

Authors and Affiliations

  1. Department of Chemistry, University of York, York, UK

    Jon Agirre, Gideon J Davies, Keith S Wilson & Kevin D Cowtan

  2. Departament de Química Orgànica and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona, Spain

    Javier Iglesias-Fernández & Carme Rovira

  3. Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain

    Carme Rovira

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  1. Jon Agirre
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Correspondence to Jon Agirre or Kevin D Cowtan.

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Agirre, J., Iglesias-Fernández, J., Rovira, C. et al. Privateer: software for the conformational validation of carbohydrate structures. Nat Struct Mol Biol 22, 833–834 (2015). https://doi.org/10.1038/nsmb.3115

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