Re: [ccp4bb] Question about the covalent Link between PLP Lysine
Sampath Natarajan wrote: I’m currently refining the structure (2.0 A) with a cofactor PLP. The PLP density is clearly indicates lysine residue is covalently bound with PLP cofactor. But I don’t know how to link the cofactor and lysine residue for further refinement. Any suggestions on how to create the link between the PLP and lysine residue and do the refinement with refmac would be greatly appreciated! My first reaction to this is check the archives! Then I tried it myself. Then my reaction was the archives are hideous - practically useless. What are jiscmail playing at? Grrr.. Anyway, those nice people in Texas save us... See the thread: http://www.hhmi.swmed.edu/Lists/ccp4-users/13971.html Paul.
[ccp4bb] Question about the covalent Link between PLP Lysine
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
Re: [ccp4bb] Question about the covalent Link between PLP Lysine
You can try JLigand from http://www.ysbl.york.ac.uk/~pyoung/JLigand/JLigand.html to create link and then add link record on your pdb Garib On 9 Oct 2009, at 03:40, Sampath Natarajan wrote: Dear All, I’m currently refining the structure (2.0 A) with a cofactor PLP. The PLP density is clearly indicates lysine residue is covalently bound with PLP cofactor. But I don’t know how to link the cofactor and lysine residue for further refinement. Any suggestions on how to create the link between the PLP and lysine residue and do the refinement with refmac would be greatly appreciated! Thanks Sincerely, Sampath N.
[ccp4bb] Question about the covalent Link between PLP Lysine
Dear All, I’m currently refining the structure (2.0 A) with a cofactor PLP. The PLP density is clearly indicates lysine residue is covalently bound with PLP cofactor. But I don’t know how to link the cofactor and lysine residue for further refinement. Any suggestions on how to create the link between the PLP and lysine residue and do the refinement with refmac would be greatly appreciated! Thanks Sincerely, Sampath N.
