The AvrRpt2 protein of the phytopathogenic bacterium Erwinia amylovora (AvrRpt2(EA)) is a secreted type III effector protein, which is recognised by the FB_MR5 resistance protein of Malus x robusta 5, the only identified resistance protein from a Malus species preventing E. amylovora infection. The crystal structure of the immature catalytic domain of AvrRpt2(EA), a C70 family cysteine protease and type III effector, was determined to a resolution of 1.85 angstrom. The structure provides insights into the cyclophilin-dependent activation of AvrRpt2, and identifies a cryptic leucine of a non-canonical cyclophilin binding motif. The structure also suggests that residue Cys156, responsible for the gene induced resistance, is not involved in substrate determination, and hints that recognition by FB_MR5 is due to direct interaction.