Unknown Residues

Hello everyone,

I am using HADDOCK ver 2.4. I would like to dock one pdb file with eight molecules to another pdb file with one molecule. Is it possible?

My second question is that when I tried that, I received a warning about some residues recorded as unknown, UNK. I have no idea how to deal with those residues. How can I know which residue they correspond to? I think I could edit those if I open the pdb file with notepad.

The error message I got is the following:
Error in PDB file.
Issue when parsing the PDB file at line 1722 .
Your PDB contains an unknown residue UNK using ATOM record, please check the HADDOCK library for a list of supported modified residues. Should this be formatted with record HETATM instead?

The pdb file with eight molecules is this one: 5FLC from PDB

Best,

Beril

Yes, Haddock can handle up to 20 molecules!

But I’m afraid you will need to do some pre-processing before submitting your docking run.

A good place to start is to check the header section of the experimentally determined structure, this mTOR complex (5FLC) was determined by cryo-em which is a “low resolution method”, depending on the resolution in which the structure was obtained, sometimes there is no way of telling which amino acid was present at a given coordinate in space. Information about this uncertainty is usually present on the PDB itself, in your target for example:

REMARK   3 OTHER DETAILS: THE UNK CHAINS (A, E, C, G, 1-4) CORRESPONDING TO     
REMARK   3  RAPTOR (A,E), SF FKBP AND RAPAMYCIN (C,G) AND THE N-TERMINAL        
REMARK   3  HEAT REPEATS OF MTOR (1-4), HAVE BEEN NUMBERED FROM 100 AT EACH     
REMARK   3  BREAK TO INDICATE LACK OF SEQUENCE - DENSITY CERTAINTY

Depending on what you want to achieve, the undetermined region could be important or maybe not. If it might be an important region important you will need to apply some method of molecular modelling to “fill the gaps”, if this region does not matter, you could remove it from the structure.

You can find more information about Haddock and the modelling methods in the Education section of our website: bonvinlab.org/education! :slight_smile: