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 <
[email protected]> 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 <[email protected]> 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
> <<[email protected]>
> [email protected]> 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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>>
>
>
>
>
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