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Figure 11
Glycosidic bond torsions can be affected by stacking interactions. (a) The most frequent conformation of the GlcNAc–Asn bond as found by Imberty & Perez (1995BB46) and Lütteke et al. (2005BB61), plotted as blue stars in (c) for PDB entry 5fji. (b) This flipped conformation of GlcNAc lies in a secondary torsional energy minimum that was originally described by Imberty & Perez (1995BB46), and is stabilized by a stacking interaction with a neighbouring tryptophan, the character of which is conserved across homologues in order to maintain the conformation of this bond (Agirre et al., 2016BB5). Stacking interactions can be computed with Privateer (Agirre, Iglesias-Fernández et al., 2015BB8), using the definition proposed by Hudson et al. (2015BB43), which states that δ must be shorter than 4.0 Å and the Ω angle must be smaller than 30°. (c) Ramachandran-like plot calculated with Privateer using the convention from Lütteke (2009BB58), also depicted here in Fig. 5[link]. This figure was generated with CCP4mg (McNicholas et al., 2011BB65).

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ISSN: 2059-7983
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