The precise accumulation of protein functions on a nanoscale to fabricate advanced biomaterials has become possible by a bottom-up approach based on molecular self-assembly. The avidin–biotin interaction is widely employed in the design of functional protein self-assemblies. Herein we assessed how the spatial arrangement of the avidin–biotin interaction between protein building blocks affects the formation of a protein supramolecular complex (PSC). The enzymatic site-specific internal labeling of a symmetric protein scaffold, bacterial alkaline phosphatase (AP), with specifically designed biotinylation substrates revealed that the precise positioning of the biotinylation sites on AP and the linker flexibility of the substrate are critical factors for the growth of PSCs in the presence of streptavidin (SA). A potential diagnostic application of the PSCs comprised of AP and SA was demonstrated in an enzyme-linked immunosorbent assay.