Heme B docking - output PDB format

HADDOCK
1

I have been docking heme B to a heme binding protein. The docking itself seems to work ok but I noticed that in the output PDB-files, “FE” is shifted to the right in the ATOM TYPE column and the right-most column says F rather than FE. As a consequence, programs such as Ligplot does not recognize the FE-atom in the centre of the heme. The input PDB-file for heme is in the correct format and the FE-atom is recognized.

I can of course easily edit the PDB-file so that the FE-atom is recognized but if the output PDB-file is wrong, perhaps the docking solutions are as well? Please advice.

Best regards,
Susanna
emphasized text

2

Did you use the web server?

There is an example of hemeB file provided in https://milou.science.uu.nl/services/HADDOCK2.2/library.html

https://milou.science.uu.nl/services/HADDOCK2.2/hemeB.pdb

3

Yes, I used the webserver and the example PDB-file provided. However, the example PDB has the same issue with the -FE atom type column and is not recognized by LigPlot. I tried to fix it by shifting “FE” one space to the left and ran the docking again but in the docking solutions it has moved back.

4

Just to clarity, if I download a heme B-containing protein from the Protein Data Bank, the FE-atom is one space further to the left in the atom type column compared to what HADDOCK provides and this is also the format that is recognized by LigPlot and Pymol. Thanks in advance.

5

That’s a ligplot issue and not HADDOCK… :slight_smile: You can always correct the HADDOCK output before running ligplot.

6

Great, that’s what I thought but I just wanted to double check :slight_smile: