Example of a small but moderately complex PDB file?

Question

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

dihedral angles
detect H, E, and C components
detect Hydrogen bonds
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?

@pippo1980, Firstly, I am only talking about secondary structures (so, turns are not discussed). Secondly, Loops and Coils are mostly synonymous. — user366312, Jun 30 '22 at 18:28
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 — gilleain, Jul 01 '22 at 14:53

score 3 · Accepted Answer · answered Jul 17 '22 at 14:14

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.

score 2 · Answer 2 · answered Jun 30 '22 at 04:19

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.

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 (http://www.cathdb.info/version/latest/domain/1ejgA00) ? — gilleain, Jul 01 '22 at 14:59

Example of a small but moderately complex PDB file?

2 Answers2