2.2 Structure modelling and molecular docking
The homology model of Mc SuSy was constructed using the YASARA
program.[30] The structures of UDP and sucrose
were obtained from ZINC database (http://zinc.docking.org/).To construct
the complex structure for evaluating the interaction between the protein
and substrates, we tested molecular docking software such as LeDock and
AutoDock Vina to dock the structure of At SuSy1 (PDB ID: 3S27,
chain A) with its substrates.[31, 32] The docking
results obtained by LeDock have a relatively good reproducibility to the
crystal structure of At SuSy1, therefore, LeDock was further used
to obtain the complex of Mc SuSy. UDP was first docked into the
active site of Mc SuSy, resulting in the structure ofMc SuSy with UDP, which was then docked with sucrose. PyMOL
(Version 2.4.1, Schrodinger LLC) was used to visualize and analyze the
model structures generated, as well as to build illustrative figures.