PDB codes for misfolded proteins?
Searching "misfolded" on the RCSB PDB turns up 64 hits. Most of these won't be relevant, but there are some interesting entries on tumor associated EGFR and misolded RNA.

In order to experimentally obtain a structure of a protein it generally has to be in a stable conformation, i.e. at low energy. Being soluble also helps. This usually corresponds to the "healthy" form, as misfolding would lead to aggregation.

That said, the structures of certain aggregates have been obtained. For example, see this recent article.

There is also the concept of mutating a protein sequence to fold to a different structure, see for instance here, though I guess you are looking for cases with the exact same sequence.