Unwanted merge of proteins chains

HADDOCK
1

Hi, I used Haddock server to dock a protein consisting of two chains (one PDB file) with DNA. Unfortunately, after the docking, the protein chains are merged into one chain only (the structure is still the same, just the annotation changed).

I would be happy about any insight into the reason or how I can prevent this.

Thanks

2

Define “merged into one chain”

It could simply be a visualisation issue

You can have TER statements between the chains. But for one molecule there will be only one chainID/segID used.
This is also the reason why there should not be any overlap in residue numbering within one molecule (even if it consists of several chains).

3

Thank you very much for the quick reply.

In the initial pdb file the protein consists of two chains A and B, after the docking all protein atoms are assigned to chain A. The overall structure and coordinates remain the same though, the two chains are fairly distant from each other (which results in a rather odd visualisation), it’s only the chain assignment that is changed.

So far I reassigned all residues from the second chain back to chain B, but I was wondering whether there is a way to avoid this in the first place.

4

So far I reassigned all residues from the second chain back to chain B, but I was wondering whether there is a way to avoid this in the first place.

Not possible - for HADDOCK each molecule must consist of a unique chainID.

5

Sorry, your question is very vague and I’m not sure I understood what you meant

In the initial pdb file the protein consists of two chains A and B

So you have two molecules with 3 chains? Which chains from which molecule do you want do use for docking?

Supposing that you have:
Molecule 1: Chain A, Chain B
Molecule 2: Chain A

And you want to use all chains of Molecule 1, on the field Which chain of the structure must be used? you’d select All, if you just want to use chain A, you’d select A.

By default Molecule 1 will become segid A, Molecule 2 segid B, Molecule 3 segid C, so on and so forth. Now, if you want your resulting complex to reflect the same chain ids of your input, you need to change it yourself. Please have a look at PDB-Tools or else you can just write a simple script to handle the renaming of the chains based on your input. :slight_smile: