Request for Assistance with Protein-DNA Docking Including Zn Ions and ACE/NME Residues Using HADDOCK

HADDOCK
1

Hello Dr. Bonvin and All

I am reaching out to seek your assistance with a protein-DNA docking analysis that I am currently undertaking using HADDOCK.

I am working with the DNMT1 protein, specifically chain A of the complex retrieved from the PDB (ID: 3PTA). My goal is to include Zn ions in this protein for the docking process. However, I have encountered difficulties in correctly introducing the charges into my PDB structure.

Could you please guide me on how to incorporate these Zn ions with the appropriate charges into the PDB file for use with HADDOCK? I have already tried several solutions that I read about, but I believe I have not correctly integrated the charges.

Additionally, I am using the YASARA server for energy minimization of my structure, but this server consistently introduces ACE and NME residues into the structure. Should I remove these residues, or is there another solution to circumvent this issue?

I am currently in a time-sensitive situation and need to complete this work urgently. Unfortunately, the bioinformaticians in my surroundings are unavailable to assist me.

I would greatly appreciate any assistance you can provide in this situation.

Thank you in advance for your valuable help.

2

However, I have encountered difficulties in correctly introducing the charges into my PDB structure.

Are you willing to use a redox state of your zinc ion or simply the standard Zn2+ ?

  • If only the Zn2+ is wished, it should be straight forward and you do not have to worry about the charges.
  • If you want to dock a redox state of your zinc, then we do not have MD parameters for it, and therefore you will have to provide parameters for it.

ACE and NME are used to neutralize the Nter and Cter residues respectively.
If you do not want them, simply edit your file and remove them by hand.

Good luck

1 Like
3

Hello,

I have added the Zn2+ ions to my file using a text editor. Regarding the ACE and NME residues, I have removed them from my PDB files of both the wild-type and mutated proteins using MyMol.

Thank you for your guidance.

Best regards,