Structural insights into a high affinity nanobody:antigen complex by homology modelling.

•In this study a homology model of a high affinity RgpB-nanobody (VHH7) was build.•Epitope residues and paratope residues were identified and used as input to an information-driven flexible docking approach.•The VHH7 binding epitope was found in the immunoglobulin-like domain.•Computational alanine scanning identified residue pairs at the molecular interface that was important for complex stability.•The molecular interaction data can be used in the design of an antibody-drug conjugate for specific RgpB targeting.