My template is a homodimer and I want to model my target also as a hmodimer. The sequence of the chain A of homodimer in the PDB file is like: MKQA.............G. The sequence of the chain B of homodimer in the PDB file is like: MKQA.............GK. The sequence of protein in the NCBI protein database is like: MKQA.............GK. I have studied how to model a protein as a dimer using modeller (http://salilab.org/archives/modeller_usage/2010/msg00273.html). But if there is a slight difference in the two chains, like in this case the K residue is extra, then what should I do? (It would show a sequence difference if I use chain copy the same alignment in both) Please suggest.
On 04/10/2011 10:07 PM, rjayashree13-science@yahoo.co.in wrote: > My template is a homodimer and I want to model my target also as a > hmodimer. > The sequence of the chain A of homodimer in the PDB file is like: > MKQA.............G. > The sequence of the chain B of homodimer in the PDB file is like: > MKQA.............GK.
If the sequences are different, then it isn't a homodimer...
> But if > there is a slight difference in the two chains, like in this case the K > residue is extra, then what should I do?
Either model it as a heterodimer (in which case you wouldn't add the Modeller symmetry restraints) or align that extra K residue with a gap in your model sequence (or add a gap to the end of the template A chain and align it with a K in your model sequence), so that the two chains are identical in the model.
Ben Webb, Modeller Caretaker
participants (2)
-
Modeller Caretaker -
rjayashree13-science＠yahoo.co.in