Hi all,
The following question was posed on the CCP4 bulletin board earlier this week:
I have a question related to protein structure, but not crystallography
per se. Has anyone see a disulfide forming between the two cys of "CXC"
in the middle of a loop, and create a sharp turn, where X is not a
proline? I seems to me that geometrically this would be possible but I
am not sure how stable it is, or how energetically unfavorable it might
be.
This is the kind of task that can be carried out quickly and easily with
PDBeMotif - and here's how to do it:
(1) Surf to PDBeMotif at http://pdbe.org/motif
(2) Click on the "Search" tab (or the "Search" link)
(3) Select the option to search "Protein sequence, pattern" by clicking on the
corresponding icon on the left of the page (fifth icon down)
(4) In the sequence box enter: CXC
(5) Select the radio button to search using "Pattern match on observed PDB
sequences"
(6) Click on "Add it to the search criteria"
If we were to carry out the current search, we would get all observed
instances of Cys-X-Cys in the PDB. However, we want to specify that the two
cysteines are covalently linked. This can be done as follows:
(7) Select the option to search "Interactions" by clicking on the
corresponding icon on the left of the page (sixth icon down)
(8) In the panel, change the two drop-down menus labelled "Interacting
residue" so that one says "1" and the other says "3" (from their default value
"any"). Also set the "Bond type" drop-down to "Covalent bond".
(9) Click on "Add it to the search criteria"
Now we have specified that we want to find instances of Cys-X-Cys, where there
is a covalent bond between the two Cys residues (residues 1 and 3 in the
pattern CXC).
(10) Before you hit the "Search" button, you can limit the search with the
"Normalise hits by" drop-down. If you select "-" you will get all instances in
the PDB; if you select "UniProt", only one entry per UniProt ID will be
retrieved, etc.
(11) Hit the "Search" button
(12) If you searched for all instances in the PDB, PDBeMotif will return a
list of 147 hits in 55 PDB entries. If you normalised by PDB header, you will
get 18 hits in 18 entries.
(13) To visualise (some of) the hits, mark the check boxes of the instances
you're interested in. Then select a visualisation program at the bottom of the
page by clicking on its icon (e.g., Jmol). All the selected hits will be
superimposed and shown in the selected viewer.
For a screendump see: http://www.ebi.ac.uk/~gerard/cxc-motif.jpg
(Note: if you're an advanced user, you may one day want to edit and submit
your queries in XML - click on "Get Query XML" for more information.)
-----
If you have any questions or comments about PDBeMotif, please use the feedback
button at the top of any PDBe web page.
--Gerard
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Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk ..................... pdbe.org
Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
