The ligand-substrate complex is situated within a hydrophobic pocket containing polar residues interacting with the substrate complex at the domain interface of each dimer.  One surface of each dimer consists of mostly polar residues, with the other surface consisting of mostly non-polar residues.  Each active site pocket consists of mainly hydrophobic residues, with the inner core of the pocket containing polar residues interacting with the substrate. Examining the secondary structure illustrates the main component of the outer surface of the protein shell is α-helical, while the active site pockets consist of β-sheet structure.

Each dimer's topology is similar to the next, consisting of one subunit forming a 2-layer "sandwich" of β-sheet and α-helix, while the other half of the dimer forms a "barrel" type shape utilizing both types of secondary structure.  There are three components to the active site of the dimer:  the floor, the wall, and the cover.  In one dimer, the floor consists of residues Phe36, Glu37, Gly38, Arg59, Lys159, Glu193, Gly196 and Leu217, the wall consists of residues Arg40, Tyr95, Arg97, Tyr164, Thr257, Ala258, Tyr31, and Val109, and the cover consists of residues Trp126 and Tyr129.

The proposed mechanism for this enzyme consists of substrate binding to the polar groups forming the active site.  This is accomplished by Arg40 interacting with the carboxyl-group of the main chain β-turn in the active site.  The Arg97 residue also plays a role by merging with the hydroxy-group to assist in the reaction mechanism. The PLP substrate's role in this mechanism is to form an L-branched chain amino-acid/Schiff Base intermediate, which can subsequently be hydrolyzed to form an α-keto acid.