In his latest paper E. Krissinel (2009). /Crystal contacts as nature's docking solutions/. J. Comp. Chem., in press; published on-line 6 May 2009; DOI 10.1002/jcc.21303
Krissinel wrote that DGdiss error is 5kcal/mol. I think that DG~5kcal/mol is a gray zone. Then he compares docking results with actual structures, a lot of failures! Is your protein exactly the same as documented or from a different species? My protein has three different oligomeric states from three different species, and the monomers from different species superpose well. Maia humayun scherrif wrote: > > Thank you all for the replies. > > * The protein itself makes hexamer which is well documented and > proved structural evidence from other cytoplasmic domains ( my > structure is also a domain). > * I have run PISA, but the online PISA server didnt give me output > like standalone PISA in CCP4 (result is mentioned below). Online > PISA results show that "there are not significant dimer > interfaces and thus the trimer structure is because of only > crystal packing result" > * For homology modeling I didnt get any proper homologs which have > hexameric assembly (I@ Bryn: I cant send you PDB id since its > not submitted yet) > > > Analysis of protein interfaces suggests that the > following quaternary structures are stable in solution (I wonder the > DGdiss is positive value, is it significant to make Hexamer assembly > because I couldnt find any help to find out about the allowed values) > > ----.-----.---------------------------------------.--------------- > Set | No | Size Id ASA BSA DGdiss | Formula > ----+-----+---------------------------------------+--------------- > 1 | 1 | 6 0 19917.7 5536.3 3.8 | A(2)B(2)C(2) > ----+-----+---------------------------------------+--------------- > 2 | 2 | 3 1 10722.9 2004.1 6.2 | ABC > ----+-----+---------------------------------------+--------------- > 3 | 3 | 4 2 14004.2 3014.9 0.5 | A(2)B(2) > | 4 | 1 3 4217.5 0.0 -0.0 | A > ----+-----+---------------------------------------+--------------- > 4 | 5 | 2 4 7506.2 1003.3 7.0 | AB > | 6 | 1 3 4217.5 0.0 -0.0 | A > ----+-----+---------------------------------------+--------------- > 5 | 7 | 2 5 7443.8 1000.8 6.8 | AB > | 8 | 1 6 4282.4 0.0 -0.0 | A > ----+-----+---------------------------------------+--------------- > 6 | 9 | 2 7 7556.5 1008.3 2.0 | A(2) > | 10 | 1 8 4227.1 0.0 -0.0 | A > | 11 | 1 3 4217.5 0.0 -0.0 | A > ----'-----'---------------------------------------'--------------- > > > Waiting for your reply > > Thanks > > > H > > > > > On Wed, May 19, 2010 at 4:41 PM, Robert Brynmor Fenwick > <robert.fenw...@irbbarcelona.org > <mailto:robert.fenw...@irbbarcelona.org>> wrote: > > Also, if you would like to try homology modelling then that could > work. However you would need a couple of hexamer strucutres to > start with. It would probably take some tinkering with current > tools. I would probably use an MD approach to solve this problem. > > Sorry I don't have a quick fix this is not my current area of > expertise. > > Bryn > > Sent from my iPod > > On 19/05/2010, at 09:22, humayun scherrif <hum....@gmail.com > <mailto:hum....@gmail.com>> wrote: > >> >> Thank you Bryn for your reply, But I have already tried all >> possible symmetries that it generates, but it does not provide a >> proper hexameric assembly. Does it mean this is due to problems >> in crystal packing ? >> >> Is there any alternative way to generate or by homology, which >> server could be suitable ? >> >> >> Regards >> >> H >> >> >> On Wed, May 19, 2010 at 4:02 PM, Robert Brynmor Fenwick >> <robert.fenw...@irbbarcelona.org >> <mailto:robert.fenw...@irbbarcelona.org>> wrote: >> >> There is a symmetry command that will build the crystal >> symmetry from >> the pdb header you could then delete the irrelevent molecules >> to leave >> the six that you want. >> >> Bryn >> >> If you have trouble with this I can hunt down the commands in >> my labbook >> >> >> > _______________________________________________ >> > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net >> <mailto:PyMOL-users@lists.sourceforge.net>) >> > Info Page: >> https://lists.sourceforge.net/lists/listinfo/pymol-users >> > Archives: http://www.mail-archive.com/pymol- >> > us...@lists.sourceforge.net >> <mailto:us...@lists.sourceforge.net> >> >> >> >> > > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------------ > > > ------------------------------------------------------------------------ > > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net ------------------------------------------------------------------------------ _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
