Issues with abasic site in DNA

HADDOCK
1

Hi Alexandre,
I have the structure of a AP-endonuclease (specific for abasic sites in DNA) and I would like to dock a DNA containing an abasic site. These enzymes are known to induce a kink at the abasic site to bind the phosphate group in the active site. Therefore, I took a structure of a kinked DNA from the PDB and tried the docking experiment with this.

The problem I have is that the abasic site is labelled as 3DR in PDB files, and is not recognized as part of the DNA by HADDOCK, so it tends to disrupt the DNA and move the 3DR around quite a bit, even if I have all the CONNECT in the pdb file. I guess the easiest way to fix this would be to run the docking with the DNA considered as a complete rigid body (including the 3DR) so that it would retain the kink. Is there a way to do this?

Thank you

Jonathan

2

This is not a supported base by HADDOCK and it is treated as HETATM. As such it is not connected to the remaining of your DNA, what introduces the disruption.

Nothing much you can do about it… You could define a few specific distance restraints to keep it in place (but if won’t be covalently linked to the remaining of your DNA).