Kunitz proteinase inhibitors are widely distributed in legume seeds, and some of them have the ability to inhibit two different classes of enzymes. In this report, novel insights into three-dimensional structure and action mechanism of ApKTI, an Adenanthera pavonina Kunitz trypsin inhibitor, were provided to shed some light on an unconventional non-competitive activity against trypsin and papain. Firstly, ApKTI was purified by two tandem-size molecular exclusion chromatography high resolutions, Sephacryl S-100 and Superose 12 10/300 GL. Purified ApTKI showed molecular mass of 22 kDa and higher affinity against trypsin in comparison to papain, while the bifunctional inhibitor presented lower inhibitory activity. Moreover, in vitro assays showed that ApKTI has two independent interaction sites, permitting simultaneous inhibition to both enzymes. Theoretical three-dimensional structures of ApTKI complexed to both target proteinases were constructed in order to determine interaction mode by using Modeller v9.6. Since the structure of no non-competitive Kunitz inhibitor has been elucidated, ApTKI-trypsin and ApTKI-papain docking were carried out using Hex v5.1. In silico experiments showed that the opposite inhibitor loop interacts with adjacent sites of trypsin (Arg(64), Ser(107), Arg(88) and Lys(108)) and papain (Gln(51), Asp(172) and Arg(173)), probably forming a ternary complex. Unusual residue substitutions at the proposed interface can explain the relative rarity of twin trypsin/papain inhibition. The predicted non-coincidence of trypsin and papain binding sites is completely different from that of previously proposed inhibitors, adding more information about mechanisms of non-competitive plant proteinase inhibitors.