β1,4-Galactosyltransferase (β4Gal-T1) transfers galactose from UDP-galactose to N-acetylglucosamine (GlcNAc) in the presence of Mn²⁺ ion. However, in the presence of α-lactalbumin (LA) it transfers Gal to glucose (Glc) instead to GlcNAc. Upon substrate binding, β4Gal-T1 undergoes transition, from an open to a closed conformation. Although both the acceptor and donor substrates can induce the necessary conformational changes, the enzyme has been crystallized only in the closed conformation in the presence of its preferred donor, UDP-Gal. The closed conformation induced by the sugar acceptors or the less preferred donor substrates has been observed only when complexed with LA. The crystal structure of β4Gal-T1 in the presence of UDP-Gal was previously determined at 2.8 Å resolution. We report here the same structure at 2.3 Å resolution, which provides a better description of this closed conformation. We have also further refined the structures of β4Gal-T1·LA complexes containing the sugar acceptor and the less preferred sugar nucleotide donor substrates and compared the conformational changes in the enzyme induced by substrates with and without LA. Based on the binding of UDP-sugar molecules, a rational hypothesis is proposed for the conformational changes induced by the donor substrate.