Modelling of auxin-binding protein 1 suggests that its C-terminus and auxin could compete for a binding site that incorporates a metal ion and tryptophan residue 44.

Sequence comparison indicates that auxin-binding protein 1 (ABP1) belongs to a family of proteins with the core beta-barrel structure of the vicilins. Previous modelling within this family correctly predicted metal-ion binding and oligomeric properties of oxalate oxidase. ABP1 also contains a putative metal-ion-binding cluster of amino acids, adjacent to a tryptophan side chain, leading to a proposed auxin-binding site that incorporates metal-ion interaction with the auxin carboxylate. Modelling implicates W44 (Zea mays ABP1) in auxin binding, rather than W136 or W151. Reduced sequence similarity for the C-terminal region prevents model building. It is proposed that one of these C-terminal tryptophans, along with a neighbouring negatively charged side chain, occupies the binding pocket in the absence of auxin, thereby linking auxin binding to conformational change and C-terminal involvement in signalling.