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I'm searching for PDB code examples for "healthy proteins" and misfolded ones, so I can compare the 3D structure. I'd prefer pairs of a "protein misfolding disease", but could be any. Can I find such a list or how should I search for the particular codes? I'm particularly interested in ones that also cointain SS-bonds.

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  • $\begingroup$ Do you mean disulphide bonds between cysteine residues ? These are really rare unless it is chemical modifcation $\endgroup$ – Michael Aug 13 '19 at 14:25
  • $\begingroup$ I'm not sure they are rare, when opening random PDB files, I often come accross disulphide bonds... $\endgroup$ – Jake B. Aug 13 '19 at 16:44
  • $\begingroup$ Hi @JakeB there is a misunderstanding. Disulphide bonds are incredibly well conserved, even in RNA viruses. Misfolding resulting from a disulphinde bond is rare. $\endgroup$ – Michael Aug 14 '19 at 14:47
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PDB 5E83 sickle cell anaemia.

All details for comparison to wildtype rbc are found in,

Oksenberg, D., Dufu, K., Patel, M.P., Chuang, C., Li, Z., Xu, Q., Silva-Garcia, A., Zhou, C., Hutchaleelaha, A., Patskovska, L., Patskovsky, Y., Almo, S.C., Sinha, U., Metcalf, B.W., Archer, D.R. GBT440 increases haemoglobin oxygen affinity, reduces sickling and prolongs RBC half-life in a murine model of sickle cell disease. (2016) Br.J.Haematol. 175: 141-153

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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.

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There are very few real structures of soluble misfolded proteins, for the reasons described by jgreener. An example with a disulfide bond is beta-2-microglobulin, eg PDB entries 2XKS vs 2XKU.

Atomic-resolution structures of amyloid fibrils may be what you're looking for, such as 6GK3 for beta-2-microglobulin amyloid (which has its disulfide intact). A search for "amyloid fibril" at rcsb.org will find many structures. But many amyloid precursor proteins are intrinsically disordered, or are fragments of native proteins.

There's no list that I know of, but here's a recent review: https://www.ncbi.nlm.nih.gov/pubmed/30237470

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