Hi
You can do this type of selection from this service at PDBe. It provides
you with many options that you can combine into a query to make selections
of PDB-ID.
http://www.ebi.ac.uk/pdbe-as/pdbeselect/PDBeSelect.jsp
From this page :
select from the drop down [Assembly] -> Assembly Name
Click [show distribution]
You will need to use the max scroll slider - drag this left to until you
see dodecamer
(it has 0.7% occurrence)
Click on the edge of the Pie to select this - it will appear on the list
to the right
Clicking on [how many entries] will tell you that as of today there are
1728 entries of this type.
From [Assembly] -> symmetry number
[Show Distribution] - will show a pie chart of symmetry-number
You need need to select the bar = 12 ; which might be easier if you
slide the
minimum scroll bar right (Note you can click and drag to select a range
here -
but not useful for your question)
This will appear in the selection on the right with the assembly name
Now click [How many entries ?]
This gives 415 entries
From the table on the right - click on the ID column cells to open the
atlas
page for any entry of interest. Go to the quaternary page on the atlas
page
to check that this correct. You can also [Get] a list of entries as
text or XML,
or put the SQL into the query browser to fine tune this.
Regards
Tom Oldfield
Check with PISA@EBI, it has database searches where you can fetch all
dodecamers in the PDB
Eugene
On 20 Feb 2013, at 06:29, Hui Wang wrote:
Dear all,
I am looking for proteins that form a dodecameric ring structure (Not two
rings of hexamer Nor tetrahedral distribution of subunit trimers). I found some
phage portal proteins after a quick search in PDB, but I need more. Does
anyone know more protein dodecamers that has C12 symmetry?
Thanks,
Hui
--
Tom Oldfield , PhD
Team Leader
Head of PDBe Databases and Services
Protein Databank in Europe
European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
Tel : ++44 (0) 1223 492526
