Ligand Protein Connection

From: Sam Arnosti <meisam.nosrati@gmail.com>
Date: 29 September 2011 22:12
To: CCP4BB@jiscmail.ac.uk
Hi every one

I have a problem with docking my ligand into the electron density map and make the connections ( bonds ) with the protein.

It is a Lysine residue that makes a Schiff Base with a long chain aldehyde.

I do not know how to make the bonds and control the torsion angles of the ligand.

I am using the CCP4 and Coot program for refining.

Thanks

Sam

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From: Wei-Chun Kao
Hello Sam,

if the ligand dictionary file is not available from the CCP4 monomer library (refmac would stop when it recognized an unknown ligand), you have to generate it from either the PRODRG server (http://davapc1.bioch.dundee.ac.uk/prodrg/) or PHENIX eLBOW (http://www.phenix-online.org/documentation/elbow.htm). Use it as LIBIN for refmac to define the restraints. Coot will also need it (File --> Import CIF dictionary) for real space refinement.

Wei-Chun

--

Wei-Chun Kao, MSc.

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From: Andrey Lebedev
Hi Sam

Except for torsion angles, here is a good tutorial for you (the second one)

http://www.ysbl.york.ac.uk/mxstat/JLigand/

Andrey

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From: Eleanor Dodson

If you build the ligand close to the LYS and run the review restraints option in REFMAC it will suggest a LINK cif file. Check it carefully and see if you agree with the supposed chemistry, then you can use it as part of your dictionary. You will need the LINKR record the program will have added to your pdb file
Eleanor