We have the classical molecular dynamics simulation of the PfK13 protein that has been associated with the ubiquitination process and antimalarial drug resistance. The protein dynamics of the WT and four mutants i.e. Y493H, R539T, I543T and C580Y have been performed and compared with each other. We have observed that despite being in the mutated site structural dynamics of Kelch-domain remain almost same for all the cases as of WT. However, we have realized that mutation in the Kelch-domain instigates larger structural fluctuation in the BTB-domain. Further, it has been noticed that specifically, the loop region of the BTB domain is the primary reason for the large fluctuation. Among all the mutants, the largest deviations in the dynamics occur only for the Y493H and C580Y. The non-covalent electrostatic His493-Glu426 interaction, as well as the secondary structure change, is also responsible for the large dynamical fluctuations in Y493H.