Re: A simple question about the protein assignment.

Ju-Seog Lee (
Sat, 16 Mar 1996 03:32:25 -0600

At 10:42 PM 3/14/96 -0800, you wrote:

>> Hi Peter
>> I don't know of an amino acid abbreviated PCA, but this is a common
>> abbreviation for "perchloric acid" or "perchlorate anion" which could be a
>> counterion in the crystal. It would most probably be complexed to the amino
>> terminus where there is a positively charged group to neutralise.
>> Terry
>Thanks for the information. In my protein, PCA is indeed found at the
>amino terminus. I am confused, however, that in the pdb file it should
>appear as an amino acid, associated with alpha and beta carbons. The pdb
>file starts as follows:
>ATOM 1 N PCA A -3
>ATOM 3 C PCA A -3
>ATOM 4 O PCA A -3
>ATOM 6 N LEU A -2

I really don't know what PCA means in relaxin. But It doesn't look like
perchloric acid to me,
since atomic component of PCA is N-Calpha-CO
which look like amino acid.
percholic acid is HClO4.
I think you really look up their published paper to know this.
J Mol Biol 221: 15-21 (1991)[92015205]

Also second PCA(NCCOCCCO)in helix C is not the same PCA(NCCOC) in helix A.
If I am wrong, pls correct me.

>Another question: Why does the residue numbering scheme start with
>negative integers?

The reason for this is we want to keep the same numbering among homologoue
Here is explanation from pdb guide.

- Homologous proteins can exist in a number of different species.
Depositors may use a residue numbering scheme in order to preserve the
homology. The reference protein may be numbered sequentially starting with
1, then the homologous protein from another species aligned to it. If
residues are not present in the homologous sequence, residue numbers may be
skipped so that alignment can be preserved. If additional residues are
present relative to the reference protein, they may have a letter, called
an insertion code,
appended to the sequence number. Negative numbers and zeros are permitted if
they are needed to align the N-terminus.

numbering of your protein(relaxin) is based on insulin.

I hope this help you.
* Ju-Seog Lee Department of Biology *
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