Hi James,
The concept of insertion code arose when one species
was sequenced and studied and then it turned out that there
were both insertions and deletions in the sequence of the
analogous molecule for some other species.
In analyzing and discussing structure, e.g. the catalytic
triad of serine proteases, it is helpful if the residue numbering
is aligned between species.
In all code using PDB entries it is important to use
the chain identifier, residue number, and insertion code
to uniquely identify a residue.
Frances
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On Tue, 3 May 2011, James Holton wrote:
My understanding is that it was introduced for cases where an error in the
sequence was discovered long after a large body of literature had accumulated
for
the "wrong" sequence. That is, imagine some enzyme where an important catalytic
active site residue was number "152", and lots of people had been talking about
this residue for years. Then, when you solve the 3D structure, you discover
that
there is actually a glycine between residues "32" and "33", what do you do? Do
you change 152 to 153 and put up with all the angry letters from enzymologists,
telling you that you mislabeled this important residue? In case you don't want
to do this, the PDB allows you to put in a residue "32A". Deletions can happen
too, but they are easier to deal with from a file format standpoint.
-James Holton
MAD Scientist
On 5/3/2011 6:27 AM, Jahan Alikhajeh wrote:
Dear Friends,
I have noticed an issue in a pdb file, the term "insertion code".
Does anyone know anything about it? what is it used for?
Thanks in Advance,
Jahan Alikhajeh, Ph.D,
Technical Supervisor,
MAN Corporation LTD,
Keshavarz Boulevard,
Ghods Avenue No. 41,
5th Floor, Tehran, Iran, 14177,
Tel: +982166282841
Fax: +982166282997
