The outer membrane protein A (OmpA) plays important roles in the pathogenesis of bacterial infections and the anchoring of the outer membrane to the bacterial cell wall. The C-terminal periplasmic domain of OmpA (OmpA-like domain) associates with the peptidoglycan (PGN) layer non-covalently manner, which is critical for the supramolecular assembly of the bacterial envelope. However, there is a paucity of information on the structural aspects of the mechanism of PGN recognition by OmpA-like domains. In order to explain this molecular recognition process, we present the high-resolution crystal structure of an OmpA-like domain from Acinetobacter baumannii bound to meso-diaminopimelic acid (mDAP), a unique bacterial amino acid from the PGN. The structure clearly illustrates two absolutely conserved Asp271 and Arg286 residues are the key to the binding to mDAP of PGN. Identification of mDAP as the central anchoring site of PGN to OmpA is further supported by isothermal titration calorimetry and a pull-down assay with PGN. Nuclear magnetic resonance (NMR) studies with synthetic PGN fragments allowed the mapping of the binding sites of the ligand onto protein structure, which leads to a computational model for the binding of PGN with OmpA. Furthermore, NMR-based computational model for complexation between the PGN and OmpA is validated by determining the crystal structure in complex with a synthetic PGN fragment. These structural data provide a detailed glimpse of how the anchoring of OmpA to the cell wall takes place in bacteria and will be helpful in understanding the dynamics of OmpA-like domains in the anchoring of the DAP-type PGN layer, which is vital for bacterial survival.