Hi Humayun, Yes, then you seem to be left with docking as the only option. There are servers for that too, but since you want to do six-body docking, you may need to contact somebody for assistance/guidance.
Cheers, Tsjerk On Wed, May 19, 2010 at 1:11 PM, humayun scherrif <hum....@gmail.com> 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> 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> >> 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> 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> 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> 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) >> >>> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> >>> > Archives: http://www.mail-archive.com/pymol- >> >>> > 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 >> > >> >> >> >> -- >> 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 > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands ------------------------------------------------------------------------------ _______________________________________________ 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
