pyroglutamate

Jiang Jiansheng jiang at LAPLACE.CSB.YALE.EDU
Fri Oct 27 22:23:02 EST 1995


> does anyone happen to have topology and parameter files for
> pyrrolidone carboxylic acid, AKA pyroglutamate,
> official PDB code PCA, synonym PGA,
> cyclic compound which sometimes forms when a glutamine appears
> at the N terminus of a polypeptide?

> does anyone happen to know how many PDB entries (and which) contain a
> pyrrolidone carboxylic acid residue (aka pyroglutamate) ?
> standard PDB residue code is PCA , synonym PGA.

Is this PCA residue that you are looking for?

The following topology file for PCA was modified
from GLN residue for the B72 Fab antibody fragment
structure. (Brady R.L. and etc. (1992).  JMB, 227. pp253-264.).
The parameter file was modified to be compatible with
the latest Engh & Hubber's parameter set ("parhcsd.pro").

When PCA is patched to the N-terminal, one has to insert
"FIRSt PCAP                TAIL + PCA     END { nter for PCA }"
after reading "toph19.pep" in the chain statement in the
"generate.inp" file.

Please let me know if you have any problem to use it.

Jiansheng Jiang.

!---------------tophpca.b72------------------------------------
REMARK PCA residue (modified from GLN)
REMARK patch to the N-terminal see the p-residue "PCAP"
REMARK for B72 Fab structure, Jiansheng Jiang, 6-SEP-91 at York

!------------------------------------------------------------------

RESIdue PCA
 GROUp
  ATOM N    TYPE=N     CHARge=-0.20   END
  ATOM CA   TYPE=CH1E  CHARge= 0.10   END
  ATOM CB   TYPE=CH2E  CHARge= 0.00   END
  ATOM CG   TYPE=CH2E  CHARge= 0.00   END
  ATOM CD   TYPE=CH2E  CHARge= 0.00   END !#
  ATOM OE1  TYPE=O     CHARge=-0.55   END !#
  ATOM C    TYPE=C     CHARge= 0.55   END
  ATOM O    TYPE=O     CHARge=-0.55   END

 BOND N    CA
 BOND CA   C
 BOND C    O
 BOND CA   CB
 BOND CB   CG
 BOND CG   CD
 BOND CD   OE1
 BOND CD   N

 DIHEdral N    CA   CB   CG
 DIHEdral CA   CB   CG   CD 

 DIHEdral CB   CG   CD   N
 DIHEdral CG   CD   N    CA

 IMPRoper CA   N    C    CB   !tetrahedral CA

 ACCEptor O C

 IC   N    C    *CA  CB     0.0000    0.00 -120.00    0.00   0.0000
 IC   N    CA   CB   CG     0.0000    0.00    0.00    0.00   0.0000

END {PCA}

!------------------------------------------------------------------

PRESidue PCAP                { this is the N-terminal for PCA residue
                               PCAP - PRO -...                      }
 GROUp
  ADD    ATOM +HT1  TYPE=HC   CHARge= 0.35   END
  ADD    ATOM +HT2  TYPE=HC   CHARge= 0.35   END
  MODIfy ATOM +N    TYPE=NH3  CHARge=-0.20   END
  MODIfy ATOM +CD             CHARge= 0.25   END
  MODIfy ATOM +CA             CHARge= 0.25   END

 ADD BOND +HT1  +N
 ADD BOND +HT2  +N

 ADD ANGLe +HT1  +N    +HT2
 ADD ANGLe +HT2  +N    +CA
 ADD ANGLe +HT1  +N    +CD
 ADD ANGLe +HT1  +N    +CA
 ADD ANGLe +CD   +N    +HT2

 ADD DIHEdral +HT2  +N    +CA   +C
 ADD DIHEdral +HT1  +N    +CA   +C

 ADD DONOr +HT1  +N
 ADD DONOr +HT2  +N

 ADD IC   +HT1  +CA   *+N   +CD     0.0000    0.00  120.00    0.00   0.0000
 ADD IC   +HT2  +CA   *+N   +HT1    0.0000    0.00  120.00    0.00   0.0000

END {PCAP}

!------------------------------------------------------------------

!---------------parampca.b72------------------------------------
REMARK estimmated parameters for PCA residue
REMARK for B72 structure, Jiansheng Jiang, 6-SEP-91 at York.
REMARK 3x-6x up to be compatible with "parhcsdx.pro"

!----------------------------------------------------
bond  CH2E  O            1200.0  1.24
angle NH3   CH2E   O      400.0 121.0
angle CH2E  CH2E   O      400.0 121.0
!----------------------------------------------------




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