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 <tsjerkw@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.one@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.fenwick@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.one@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.fenwick@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
>>>
>>>
>>> > _______________________________________________
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>>> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> > Archives: http://www.mail-archive.com/pymol-
>>> > users@lists.sourceforge.net
>>
>>
>>
>
>
>
>
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--
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.one@gmail.com