Dear All,
I have been trying to generate physiological relevant Hexameric structure of
my recently solved trimer structure by using Symmetry Mates in Pymol, but I
am unable to find appropriate hexamer even with all type of symmetry options
available in Pymol (different distances)
Surface contact o
Hi Humayun,
are you sure the protein is hexameric?
Didn't PISA give you a hexameric assembly for your structure?
Cheers,
Thomas
On Wed, 2010-05-19 at 15:12 +0900, humayun scherrif wrote:
> Dear All,
>
> I have been trying to generate physiological relevant Hexameric
> structure of my recent
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
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
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 c
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 wrote:
> Hello,
> Tha
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 wi
Thank you all and certainly seems llike now I am going to some right
direction.
I have read some discussion part (page 14) of the paper Maia sent, as stated
below, the BSA ( value for my dimer interfaces are ~1000 (as predicted by
PISA) which according to the Krissinel paper, is biological relevan
