James, interesting that you chose residue number 32 for your example, because that is the number of one of the two active-site ASPs in the aspartic proteinase family (the other is ASP 215) that I (with Tom Blundell & others) worked on for many years. So Ed, it's not just relevant to the "Wu&Kabat numbering for antibodies". The idea that one would _not_ use consistent numbering (and therefore insertion codes) across species (viral, fungal, plant and animal so there is huge sequence variability with insertions & deletions everywhere), when working with these structures is frankly ludicrous. I recall some programs (FRODO was one) actually required renumbering to the ordinals, i.e. 1, 2, 3 ... - that is until I fixed it! This caused endless confusion, not least because there are often other ASPs in the vicinity of the active site which could easily get renumbered to 32. For me, it's important that when I refer to 'ASP 32' there's no possibility that I mean anything other than the active site ASP!
Cheers -- Ian On Tue, May 3, 2011 at 5:17 PM, James Holton <jmhol...@lbl.gov> 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 > >
