Dear community,
- I am currently working on the crystal structure of FOKI. https://doi.org/10.2210/pdb2FOK/pdb
- Unfortunately, the researches who made the crystal structure havent been able to crystalize the Amino acid at position 79 due its location in a variable loop. While I am able to align basic structures and introduce new amino accids, I have not been able to move the newly generate amino acid to the position within the structure.
- Could anybody may help me with this ?
There are several ways to perform the operation you need. I am assuming only residue 79 is missing. "Missing" residues in crystal structures are common (disorder of some sort). One of the ways is to use some software that will generate the missing stretch (missing residue in that case). I vaguely remember that "Modeller" can do that, and I think also Schrodinger's Maestro (you may need to request a demo version from the Schrodinger company). Other ways include finding other 3D structures from the PDB in which the missing residue is found. The 3D structures must be superposed to the one you are interested in (I use ccp4mg for that). Also the local stretches around the missing residue must be in very similar conformations. Once the superposition is done, then one edits the superposed pdb, extracts the coordinates of the residue of interest, place these into the pdb with the missing residue. Normally the geometry around that site isn't quite appropriate so that local regularization (a stretch of 3 to 5 residues) is performed using the program Coot.
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