On Tue, Oct 23, 2012 at 9:55 AM, Meindert Lamers <[email protected]> wrote: > Is there any convention on the numbering of residues in a fusion protein? > > I have a structure of two domains fused together but would like to keep the > biological numbering intact. > 1st domain: residue 200-300 (protein A). > 2nd domain: residue 170-350 (protein B). > The fusion is between A300 and B170 > > Is it OK to label them chain A and B and create a LINK between the two (thus > keeping the biological residue number intact). > Or do I have to start the 2nd domain with residue number 301 (and loose all > biological information).
You could use the insertion code: the first domain could be residues 200A - 300A, the second domain would be residues 170B - 350B, e.g. ATOM 2743 CA THR A 300A -9.899 6.476 21.720 1.00 27.53 C ATOM 2750 CA VAL A 170B -6.589 4.599 21.939 1.00 32.82 C but the chain ID stays the same, with no BREAK or TER record (and no LINK required). The insertion code can be a pain to deal with from a programmer's perspective, and it makes it more difficult to specify residue ranges, but I think this is exactly what it's supposed to be used for. -Nat
