On 21/09/2023 18:05, Kelvin Lau wrote:
Dear all
I am having trouble with an unnatural ligand/amino acid.
I have a structure very similar to PDB 6Q6H, 7TQR. They all have an MDO residue
that replaces three residues in a series G-A-S-G-D to become G-MDO-D. MDO is in
the Coot library.
I have
And in fact it doesnt..
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
MDO MDO
"{2-[(1S)-1-aminoethyl]-4-methylidene-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic
acid"
Check the dictionary has labelled it as peptide
like ALA
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
ALA ALA ALANINE *peptide* 13 6 .
On Thu, 21 Sept 2023 at 18:58,
Dear all
I am having trouble with an unnatural ligand/amino acid.
I have a structure very similar to PDB 6Q6H, 7TQR. They all have an MDO residue
that replaces three residues in a series G-A-S-G-D to become G-MDO-D. MDO is in
the Coot library.
I have been very used to replacing cysteines with
Hi Eleanor
Thanks for catching that..
I was under the impression that when I am fetching the monomer, MDO, it was
defined as a peptide, not a non polymer … at least that’s what is listed here:
https://www.rcsb.org/ligand/MDO
I guess I have to go about as Paul suggested as changing it to
On 21/09/2023 21:56, Eleanor Dodson wrote:
And in fact it doesnt..
Wasn't that implied by my reply?
:-)
Paul.
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On 21/09/2023 22:25, Kelvin Lau wrote:
Hi Eleanor
Thanks for catching that..
I was under the impression that when I am fetching the monomer, MDO,
it was defined as a peptide, not a non polymer … at least that’s what
is listed here: https://www.rcsb.org/ligand/MDO
I guess I have to go about
Hi Kelvin,
the 'group' in the monomer library do not necessarily correspond to the 'type'
in CCD. The reason was that stricter rules for peptides and other groups were
applied to the library.
For MDO, there are 2 links: MDO-pept and pept-MDO to deal with this in a
polypeptide.
Of course, you
On 21/09/2023 18:58, Paul Emsley wrote:
On 21/09/2023 18:05, Kelvin Lau wrote:
Dear all
I am having trouble with an unnatural ligand/amino acid.
I have a structure very similar to PDB 6Q6H, 7TQR. They all have an
MDO residue that replaces three residues in a series G-A-S-G-D to
become
