[phenixbb] Coot mutation of Asp residue to isoAsp residue

Xiao Lei xiaoleiusc at gmail.com
Tue Aug 18 10:42:09 PDT 2015

Hi Zhijie,

Thank you very much for the information. For step 1 you mentioned, I can
get monomer with L-Asp but it seems I can not drag it (or I do not know how
to do) and can not delete or modify it to become isoAsp. I will try play
around more though.


On Mon, Aug 17, 2015 at 6:33 PM, Zhijie Li <zhijie.li at utoronto.ca> wrote:

> Hi Xiao,
> IsoAsp is essentially an L-Asp linked with next aa through its side chain
> (beta) carboxyl. So the mutation button won’t help you. You need to build
> in a new L-ASP, which is treated as a covalently linked ligand (HETATM
> records), instead of a standard residue (ATOM records) of the protein chain.
> A practical method might be: 1) delete the original Asp, 2) import a free
> L-Asp using “get monomer”, delete its hydrogen atoms and drag it into the
> density, delete one oxygen atom on the beta-carboxyl and change the
> residue’s numbering and chain id to fit it into the sequence,  3) edit the
> PDB, if necessary, to turn the ASP into a ligand (a HETATM record inside
> the chain).
> For step 3, you may need to rename the ASP to something else (IAS was used
> for isoASP in older pdb, so I would go with IAS ) so that coot won’t try to
> make a regular peptide bond using its main chain carboxyl during real space
> refinement. Of course you will need to make a cif file for the “new”
> compound too. I guess you can make a copy of ASP.cif from the monomer
> library and change everything in it to IAS. I think if you have placed the
> IAS to the right location and its ends are in bonding distance with the
> neighbouring aa residues you may not need to do anything for refmac. For
> phenix.refine you will need to add a bond description to the .edit file for
> each linkage the IAS makes to the neighboring aas.
> You may take a look at the structure 1AT6 and its PDB file. The residue
> IAS 101 is an example of isoASP. Note that the IAS atoms are HETATM in the
> chain and there are two LINK records in the header to indicate its linkage
> to neighbouring aas (LINK records are normally not generated or needed
> during refinement using refmac or phenix.refine).
> Zhijie
> *From:* Xiao Lei <xiaoleiusc at gmail.com>
> *Sent:* Monday, August 17, 2015 6:50 PM
> *To:* PHENIX user mailing list <phenixbb at phenix-online.org>
> *Subject:* [phenixbb] Coot mutation of Asp residue to isoAsp residue
> Dear Phenixbb members,
> I suspect one Asp residue in my model may be an isoAsp (isomerization of
> Asp). I am asking if there is way to mutate Asp residue to
> isoAsp(isoaspartic acid) residue in coot GUI (I'm using coot 0.8.1 EL in
> Mac OS X10.10.5)?
> I know there is a mutation button on coot, but the mutated aa lists are
> all natural amino acids. If I have to delete the Asp residue first and then
> build isoAsp into the density map, is there a way in coot to build an
> isoAsp residue in map?
> Thanks ahead.
> Xiao
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