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

Reply via email to