For DNA molecules, topological complexity occurs exclusively as the result of knotting or linking of the polynucleotide backbone. By contrast, while a few knots and links have been found within the polypeptide backbones of some protein structures, non-planarity can also result from the connectivity between a polypeptide chain and inter- and intra-chain linking via cofactors and disulfide bonds. In this article, we survey the known types of knots, links, and non-planar graphs in protein structures with and without including such bonds and cofactors. Then we present new examples of protein structures containing Möbius ladders and other non-planar graphs as a result of these cofactors. Finally, we propose hypothetical structures illustrating specific disulfide connectivities that would result in the key ring link, the Whitehead link and the 51 knot, the latter two of which have thus far not been identified within protein structures.