Crystals of the inactive mutant Glu257→Ala of cyclodextrin glycosyltransferase were soaked with the cyclodextrin (CD) derivative S-(α-d-glucopyranosyl)-6-thio-β-CD. The structural analysis showed its β-CD moiety with no density indication for the exocyclic glucosyl unit. For steric reasons, however, the position of this unit is restricted to be at only two of the seven glucosyl groups of β-CD. The analysis indicated that the enzyme can cyclize branched α-glucans. The ligated β-CD moiety revealed how the enzyme binds its predominant cyclic product. The conformation of the ligated β-CD was intermediate between the more symmetrical conformation in β-CD dodecahydrate crystals and the conformation of a bound linear α-glucan chain. Its scissile bond was displaced by 2.8 Å from the position in linear α-glucans. Accordingly, the complex represents the situation after the cyclization reaction but before diffusion into the solvent, where a more symmetrical conformation is assumed, or the equivalent state in the reverse reaction. Furthermore, a unifying nomenclature for oligosaccharide-binding subsites in proteins is proposed.