Background: Diphtheria toxin, as a critical therapeutic factor in immunotoxins development, is consisting of two parts A and B. The A fragment is containing the active site of this toxin, which are considered in this study for the evaluation the stability of it in separated situation. Material and Methods: At the first step, 3D structure of the toxin with the ID: 1XTD was retrieved from PDB. Discovery Studio3.0 Client was used for removing the water molecules, ligands and catalytic domain from the intact toxin. Simulation of catalytic domain compared to intact diphtheria toxin, were performed using GROMACS5.07, gromos96 43a1 force field. It was performed in 310°K for NVT, NPT, MD; and 2ns of time for MD step. RMSD and RMSF plots were drawn by excel. Moreover, the alignment structures of the catalytic domain and intact toxin were shown by Pymol software. Results The result of RMSF plot indicate that the about 11% of the amino acids of the catalytic domain is more than of them in the native structure. On the other hand, this plot showed that the differences in the RMSF values for about 15 amino acids is greater than 0.1. More analysis demonstrate that the RMSF values of five amino acid from six of them, which are situated in the active site of the catalytic domain, are less than of them in the intact toxin. Conclusion: In general, the results of this investigation indicate that the stability of the catalytic domain as well as active site, in separated form, is more than of them in intact toxin.

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