Just giving this thread a title.
James
On May 3, 2011, at 10:06 AM, Ian Tickle wrote:
> 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 <[log in to unmask]> 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
>>
>>
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