These dodecins are a good examples: PDB 2V21 and the like The dodecin from Thermus thermophilus, a bifunctional cofactor storage protein. Meissner, B., Schleicher, E., Weber, S., Essen, L.-O. Journal: (2007) J.Biol.Chem. 282: 33142 PubMed: 17855371 DOI: 10.1074/jbc.M704951200 Good luck
Harm --- Harm Otten, PhD Thingvalla Allé 1, st.tv. DK-2300 Copenhagen mobil +45 50 30 76 39 mail [email protected] web www.harmotten.com Please consider the environment before printing this email. On Wed, Feb 20, 2013 at 1:56 PM, Tom Oldfield <[email protected]> wrote: > 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
