[gmx-users] Topology for pyroglutamic acid

Lieven Buts 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
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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