Significance Protein interactions mediated by modular domains, such as PDZ and SH2 domains, play critical roles in biology. The modules typically recognize a linear motif in their ligands, with a few residues in the motif determining the specificity. We report a crystal structure of the complex between the cytoplasmic region of PlexinB2 and the PDZ domain of PDZ–RhoGEF. The structure shows that, in addition to the PDZ/motif interaction, a secondary interface is formed between the three-dimensional domains of the two proteins. We further show that the secondary interface enhances the affinity between plexin and PDZ–RhoGEF and is important for plexin signaling. Our analyses suggest that secondary interface-mediated interactions may be a broadly used mechanism for modular domains to achieve high specificity.