Dear Sampath!Refmac5's dictionary uses LLP to encode the "LYSINE-PYRIDOXAL-5*-PHOSPHATE", a modified lysine residue with its NZ- amino group covalently bound via a Schiff base to a pyridoxal phosphate.
See http://www.ccp4.ac.uk/html/refmac5/dictionary/list-of-ligands.html
Have a look at the attached file "LLP.pdb" (e.g. in PyMOL).In Coot, move your PLP towards the NZ of the active site LYS. Superimpose the aldehyde oxygen of PLP onto the NZ. Save both structures and replace the ATOM coordinates of the modified LYS with a HETATM record as you can see in the file "LLP.pdb" using the coordinates of your LYS and PLP accordingly. Wherever this modified LYS appears in three letter code in your PDB-file replace it by LLP. You might need to correct the atom numbers accordingly. The use this structure for refmac.
Greetings, Christian Biological Chemistry, TU Munich
LLP.pdb
Description: Protein Databank data
