Plasmodium falciparum plasmepsin X (PfPMX), involved in the invasion and egress of this deadliest malarial parasite, is essential for its survival and hence considered as an important drug target. We report the first crystal structure of PfPMX zymogen containing a novel fold of its prosegment. A unique twisted loop from the prosegment and arginine 244 from the mature enzyme is involved in zymogen inactivation; such mechanism, not previously reported, might be common for apicomplexan proteases similar to PfPMX. The maturation of PfPMX zymogen occurs through cleavage of its prosegment at multiple sites. Our data provide thorough insights into the mode of binding of a substrate and a potent inhibitor 49c to PfPMX. We present molecular details of inactivation, maturation, and inhibition of PfPMX that should aid in the development of potent inhibitors against pepsin-like aspartic proteases from apicomplexan parasites.49c inhibitor, apicomplexan parasite, P. falciparum, plasmepsin X, zymogen Abbreviations: PM, plasmepsin; RBC, red blood cell; Pfpro-PMX, Plasmodium falciparum plasmepsin X with truncated prosegment; Pfm-PMX, Plasmodium falciparum plasmepsin X mature domain; TgASP, Toxoplasma gondii pepsin-like aspartic protease or toxomepsin; UD, uncharacterized domain.Pooja Kesari and Anuradha Deshmukh contributed equally to this study.