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I am developing a bioinformatics framework only for learning purposes. I want to calculate --

  1. dihedral angles
  2. detect H, E, and C components
  3. detect Hydrogen bonds
  4. etc.

Therefore, I want a PDB file that represents a protein with a small chain but is complex enough for me to experiment with.

Can you suggest such a PDB file?

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  • $\begingroup$ detect H, E, and C components ? what are they ? $\endgroup$
    – pippo1980
    Jun 30, 2022 at 14:45
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    $\begingroup$ @pippo1980, Helix, Sheet, Coil. $\endgroup$
    – user366312
    Jun 30, 2022 at 16:35
  • $\begingroup$ was missing the E. What about Turns and Loops $\endgroup$
    – pippo1980
    Jun 30, 2022 at 18:22
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    $\begingroup$ @pippo1980, Firstly, I am only talking about secondary structures (so, turns are not discussed). Secondly, Loops and Coils are mostly synonymous. $\endgroup$
    – user366312
    Jun 30, 2022 at 18:28
  • $\begingroup$ Turns may not be SSEs (although they are related) but it may be worthwhile detecting them anyway, as it is fairly simple to check for a Calpha-Calpha distance less than 4Å $\endgroup$
    – gilleain
    Jul 1, 2022 at 14:53

2 Answers 2

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Although Insulin is a great, well studied example of a small structure it does have the slight downside of not having any sheet structure in the monomer. There is a small cross-chain sheet between residues 24-26 in both the B and D chains (from https://www.ebi.ac.uk/pdbe/entry/pdb/1zni/ ).

Another possibility might be crambin (http://www.cathdb.info/version/latest/domain/1ejgA00) which does have a small antiparallel sheet, although it is tiny at only 2 residues per strand.

A more general approach might be to use something like the top2018 structure set from the Richardson lab (https://zenodo.org/record/5777651#.YtQB59LMJH4) . I used the top500 back in the day, and they are a high-quality set of structures.

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Insulin, perhaps?

https://www.rcsb.org/structure/1trz

From here:

Insulin is a perfect molecule for exploring protein structure. It is small enough that you can display all of the atoms and still have a picture that is not too confusing. Human insulin is pictured here, using entry 1trz. This structure, like many other insulin structures, includes a hexameric complex of the hormone, and only one monomer (composed of one A-chain and one B-chain) is shown here. In the structure, you can see many of the key features that stabilize protein structure. Carbon-rich amino acids, like leucine and isoleucine, cluster in the middle of the molecule, forming a hydrophobic core, and the surface is covered with charged amino acids like arginine and glutamate that interact favorably with the surrounding water. Also notice the three disulfide bridges between cysteine amino acids, which stabilize this tiny protein.

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  • $\begingroup$ Although an excellent, canonical example ... it does have the slight downside of not having any sheet structure. It does have an bit of extended chain (shown as an isolated strand in the RCSB link). Maybe crambin (cathdb.info/version/latest/domain/1ejgA00) ? $\endgroup$
    – gilleain
    Jul 1, 2022 at 14:59
  • $\begingroup$ Can you please add this comment as a separate answer? $\endgroup$
    – gringer
    Jul 1, 2022 at 19:52

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