[gmx-users] Topology for pyroglutamic acid
lieven at ultr.vub.ac.be
Tue Jun 4 12:38:58 CEST 2002
Erik Lindahl wrote:
> Lieven Buts wrote:
> > In one of the proteins I am looking at the N-terminal
> > glutamine residue has undergone cyclisation to pyrrolidone
> > carboxylic acid (PCA), also known as pyroglutamate (PGA):
> I have opls-aa working and currently I'm debugging it. I'm pretty sure
> there are special types for 4- and 5-member cyclic amines, so I'll see
> if I can implement PCA/PGA as a terminus.
> Which name is more common, and are there any other similar
> rearrangements you need?
Well, the PDB ligand dictionary uses residue type PCA, although
they call it "pyroglutamic acid":
RESIDUE PCA 16
CONECT N 3 CA CD HN
CONECT CA 4 N CB C HA
CONECT CB 4 CA CG 1HB 2HB
CONECT CG 4 CB CD 1HG 2HG
CONECT CD 3 N CG OE
CONECT OE 1 CD
CONECT C 3 CA O OXT
CONECT O 1 C
CONECT OXT 2 C HXT
CONECT HN 1 N
CONECT HA 1 CA
CONECT 1HB 1 CB
CONECT 2HB 1 CB
CONECT 1HG 1 CG
CONECT 2HG 1 CG
CONECT HXT 1 OXT
HET PCA 16
HETNAM PCA PYROGLUTAMIC ACID
FORMUL PCA C5 H7 N1 O3
Residue type PGA is used for 2-phosphoglycolic acid.
So, PCA is probably the best abbreviation, to be
compatible with the PDB conventions.
I can't think of any other unusual residues I need
at this time.
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