Dear CCP4 BB,
We solved one co-crystal structure of a protein and a compound. We found this
compound could covalently modify an asparate residue of this protein. A
covalent bond formed between a oxygen atom of Asp carboxyl group and a carbon
atom of that compound. Does anyone knows how to draw
The easy way is Coot
Extensions Link two atoms which should create a Link record in the pdb.
I think the better way is use jligand which creates a full dictionary
describing the particular link with proper restraints.
Load your ligand, load the Asp monomer
link the two atoms in question
create t
If you feed it into REFMAC with review restraints mode - it will create a
bond between two atoms within bonding distance and write a LINKR record
into the output PDB.
You can then use that coordinate file and the LINK dictionary to refine the
model
There are other ways using the up-to-the-moment
4:19
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Creating a covalent bond
>
> Dear CCP4 BB,
>
> We solved one co-crystal structure of a protein and a compound. We found
> this compound could covalently modify an asparate residue of this protein. A
> covalent bond formed between
