Docking is very non-reliable. 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
Maia humayun scherrif wrote: > Hello, > > Thank you for detailed explanation, surely it is helping me to sort > out the possibilities. As per your query > > a) There are many references that the protein is a Hexamer, but I am > considering, because the domain which I have got structure, interacts > with other proteins to make a biological complex, their interaction > could be important for biological hexamerization of the whole complex > ( those interacting proteins also exist as hexamer in complex with my > protein ) > > b) I coudnt find any hexameric homologue (although there are some good > homologue structures but they mostly exist as dimer or monomer) > > c) the structure is not yet been solved and not reported as yet. > > So according your reply, does that mean the only possibility left is > docking ? because others are not working for me at all. > > Thank you again for suggestions. > > > > > > > On Wed, May 19, 2010 at 6:31 PM, Tsjerk Wassenaar <tsje...@gmail.com > <mailto:tsje...@gmail.com>> wrote: > > Hi Humayun, > > Crystallograpic symmetries are often not of much help to construct > biologically relevant complexes. Do you have (a) a reference of the > hexameric structure, or (b) of a hexameric homologue, or (c) is it > only known to form hexamers and is the structure still unsolved? In > case of (a), the structure is likely to have a recipe to build the > biological unit (possibly as REMARK 350 in the PDB file). In case of > (b), you can try to fit copies of the structure onto each chain of the > homologue, being aware that that will give you a crude approximation > as starting point for further work. And in case of (c), you might want > to consider doing some docking. > > Hope it helps, > > Tsjerk > > > On Wed, May 19, 2010 at 10:26 AM, humayun scherrif > <hum....@gmail.com <mailto:hum....@gmail.com>> 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 > <mailto: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 > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Molecular Dynamics Group > Groningen Institute for Biomolecular Research and Biotechnology > University of Groningen > The Netherlands > > > > > -- > Best Regards, > > Humayun Sharif > MS candidate > Protein Structure and Function Laboratory > Gwangju Institute Of Science & Technology, > Gwangju, 500-712, Republic of Korea > Email: hum....@gmail.com <mailto:hum....@gmail.com> > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------------ > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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
