Dear Prem, Defaults are very useful, but I also get very annoyed if it is not possible to overrule them, even if it is just to test some hypothesis. In your case I would try another program to generate the restraints, e.g. Grade from Global Phasing.
The PKa’s from active site residues can be very different from their PKa’s free in solution. However, with protein crystallography, you won’t be able to see the protons, so all you can do is to use your chemical intuition and maybe ask an organic chemist to come up with a plausible hypothesis. If you could get your compound 15N labeled, you might use NMR spectroscopy to find out about the protonation state, but it all depends on the reaction your protein carries out. If it turns out that this reaction cannot be performed on a protonated substrate, you must assume that it is deprotonated when bound in the active site. Cheers, Herman Von: CCP4 bulletin board [mailto:[email protected]] Im Auftrag von Prem Prakash Gesendet: Freitag, 8. August 2014 07:32 An: [email protected] Betreff: Re: [ccp4bb] Jligand help With due respect ! I want to ask that, If it is protonated at neutral pH, what about the local pka of the active site key residues involved ? would not it make any difference if it adds extra H-atom and actual case is different when the reaction is carried out ? With Kind regards Prem On Fri, Aug 8, 2014 at 4:21 AM, Boaz Shaanan <[email protected]<mailto:[email protected]>> wrote: Hi, A trick that has worked for me a few times is to skip the regularization stage in Jligand, although some may argue that it's "illegal". If your ligand/cofactor has a decent geometry without regularization it may well work for you too. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: [email protected]<mailto:[email protected]> Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________ From: CCP4 bulletin board [[email protected]<mailto:[email protected]>] on behalf of Abhinav Kumar [[email protected]<mailto:[email protected]>] Sent: Thursday, August 07, 2014 8:04 PM To: [email protected]<mailto:[email protected]> Subject: Re: [ccp4bb] Jligand help Thanks Ian. Is it possible to force Jligand to keep only two hydrogens in this case? I tried setting the N's charge to 0, but it reverts back to 1 after regularization. Thanks, Abhinav ______________________________________ Abhinav Kumar, Ph.D. The Joint Center for Structural Genomics MS99, SLAC National Accelerator Laboratory 2575 Sand Hill Rd, Menlo Park, CA 94025 (650) 926-2992 On 08/07/2014 10:02 AM, Ian Tickle wrote: Hi, I would say three: aliphatic amines such as the one you show are weak bases so at neutral pH the protonated form predominates. Aromatic amines are obviously trickier. Cheers -- Ian On 7 August 2014 17:37, Abhinav Kumar <[email protected]<mailto:[email protected]>> wrote: Hi, I am making a ligand in Jligand (figure attached) and have a question about valency of nitrogen. Jligand puts three hydrogens on nitrogen N1 when the ligand is regularized. Should there be two hydrogens or three? -- Thanks, Abhinav ______________________________________ Abhinav Kumar, Ph.D. The Joint Center for Structural Genomics MS99, SLAC National Accelerator Laboratory 2575 Sand Hill Rd, Menlo Park, CA 94025 (650) 926-2992<tel:%28650%29%20926-2992>
