Acinetobacter baumannii is one of the opportunistic bacteria contribute to burn infections. Type II toxin-antitoxin systems (RelEB) are the particular type of toxin-antitoxin modules which take part in different kinds of cellular actions in A. baumannii. Treating burn wounds with antimicrobial agents such as antibiotics forms one of the most recent crucial issues. Recently, Antimicrobial Photodynamic Therapy (aPDT) is considered as the adjuvant and innovative method for conventional antibiotic therapy. In this study, we evaluated the potential of the hierarchical nature of RelE as an antitoxin protein associated with virulence factor in A. baumannii using a number of bioinformatics tools and computer simulation molecular modeling. The predicated structure of RelE exhibited that it is a cationic protein with positive charge (1.1) in pH 7. Random coil was dominate other secondary structures in RelE which was located outside the cell. Based on the results of this study, RelE as a stable protein has a potential site for aPDT.