On Tue, Oct 23, 2012 at 9:55 AM, Meindert Lamers
<[log in to unmask]> 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
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