Which one is the smallest but the most complex PDB file?

Question

[user366312]

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?

Answer 1

[Wayne]

OCA's home page has a report that is generated weekly using PDB data where the PDB entries are broken down by file size - File size Distribution on ALL PDB entries. The PDB codes for the smallest files are listed for sizes where there are 20 or less representatives and man of those are on the small side.

The structure visualization package Jmol/JSmol includes crambin 1crn.pdb among the example files distributed with the software. It is just 4.74 Kda / 46 amino acids. It has both alpha-helices and beta-sheets, along with three disulfide bonds, represented in it. FirstGlance in Jmol quickly provides a good explorable overview of the structure right in your browser here. For example, the disulfide bonds are immediately shown in the initial view and you can further explore that by clicking on the 'Tools' tab and selecting 'Disulfides/S/Se..' from the tool options listed at the top.

Answer 2

[Mensur Dlakic]

This is an open-ended question, so most people will likely give you their favorite protein. Here goes:

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

What you are trying to do has been done many times before. Not saying it is not worth doing it from the scratch if your goal is to learn, but it may be just as effective (and faster) to look through the code others have developed. BioPython has modules that do most things you want from PDB files.

https://biopython.org/docs/dev/api/Bio.PDB.html

If you really want to go at it from the scratch, some ideas in the following links may help:

• https://biopython.org/wiki/GSOC2010_Joao
• https://biopython.org/wiki/Scriptcentral