Conformation at the binding site

Another alternative, ligand-steered homology modeling was recently introduced by Cavasotto et al. [19]. This method includes an extensive sampling of possible ligand orientations and conformations and side-chain conformations at the binding site. 

The structural differences between the R- and T-form are strongest at the interface between the dimers and impact heavily the binding site for fructose-6-P. At the binding site for the second substrate, ATP, there are only minor structural differences between the two conformations. Overall, the transition from R- to T-form is accompanied by a rotation of the two dimers aroimd the small interface the large contact surface within a dimer remains relatively imchanged. 

The ligand is modeled in a single (bioactive) conformation that exerts the binding effects. The dynamic nature of this process, as shown for lactate dehydrogenase that assumes different conformational states at the binding site [65], is typically ignored. 

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