I am working with protein which have isopeptide bonds in them and I am not sure how to handle them.
An isopeptide bond is when a lysine residue forms an amide bond with an aspartate or asparagine (same result). Isopeptide bonds —in bacteria at least— have an O or N atom missing from the Asp, Asn or Lys and a CONECT at the end of the file and to the best of my knowledge there is no special HETATOM O-lysylaspartyl double residue.
Attached is a pdb (from 2X5P) that has been cleaned up, sent through Relax and the isopeptide brutally readded (cf. in pymol `zoom resi 31+117`), so it is not a file thing.
I want to use isopeptide bonds in Relax, Remodel and Score. I can get away with K31A D117N in some applications, but for others there is no escape as the result is rather meaningless.
The problem is that a warning is raised and the residues separated. Adding a constrain does not seem to work as having an oxygen and a nitrogen superimposed messes up the scores. I tried making a lys to ornithine (Orn = C40 in the rotlib) as it would form a salt bridge and constraint the epsilon N of Orn and an O of CG of Asp. Unfortunately there is a bug in the code itself that makes it end up looking for a file with '//' error in the path name.
＄ ＄ROSETTA/relax.＄ROSETTAEXT -database ＄ROSETTADB -s 2X5Pmle2_C40_ATOM.pdb
core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.516341 seconds to load from binary
core.pack.rotamers.SingleNCAARotamerLibraryCreator: Reading in rot lib /Users/matteo/Coding/rosetta/main/database//rotamer/ncaa_rotlibs/ncaa_rotamer_libraries/alpha_amino_acid/C40.rotlib...
Segmentation fault: 11
So I was hoping to get some suggestions on how to tackle the problem of isopeptide bonds.