Selenocysteine In Pdb File

Question

[alvieirajr]

Hi!. Is normal replace the Selenocysteine (code: SEC, see) by a Alanine (ALA) ?

To the 1GP1 Entry in the PDB databank I see in PDB file the part:

> "SER LEU ***SE7*** GLY THR THR VAL ARG"

but i go to the fasta file i found this :

> SL **A** GTTVR

changed SE7 by A. This is normal ? It's correct ? I think the cause of this change is because in multiple alignment we don't have the entry to Selenocysteine in blosum matrix.

You agree ?

FASTA: http://www.rcsb.org/pdb/files/fasta.txt?structureIdList=1GP1

PDB: http://www.rcsb.org/pdb/files/1GP1.pdb

Answer 1

[Neilfws]

You are almost correct, except that SE7 (not SEC) is 2-amino-3-selenino-propionic acid (not selenocysteine), also known as 3-selenino-L-alanine.

Since it is a modified alanine, the 1-letter code remains A.