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Here is the 3D structure of TR. The protein is 968 residues; it has 32% helices and 24% beta strands. The rest consists of turns . TR is a dimer; each subunit consists of Domain I, which contains FAD , Domain II, which binds NADPH , and Domain III, which is the interface of the two subunits . The active sites lie at the bottom of each cleft between domains I and III in each subunit ; it has an overall negative charge to complement the positively charged substrates. FAD lies alongside the active site with the isoalloxazine ring exposed at the bottom .

In each subunit the residues holding FAD in the protein show a beta-alpha-beta-alpha-beta Rossmann fold that is common in nucleotide binding . The Rossmann fold contains the consensus sequence Gly-X-Gly-X-X-Gly that is usually seen in binding FAD. Ser15 and Gly16 hydrogen bond with the phosphate groups while Asp327 interacts with the ribityl chain . Gly326 turns the polypeptide chain to accommodate the phosphate groups , and Phe199 shields FAD from the environment . This side chain swings out of the way when NADPH binds to the protein to allow access to the substrate. NADPH delivers its electrons to FAD, which are then used to reduce the disulfide trypanothione (TS2) back into two molecules of trypanothione. See these residues in spacefilling model .

The presence of FAD in trypanothione reductase reduces the energy needed for this reaction; its progress is only dependent on the enzyme binding its substrate, because the FAD is always there.