Search on Database

Users can search on the database by three ways: PDB ID, Pfam ID (Accession code) and Sequences.

• PDB ID

  Input a PDB ID to find the Pfam architecture of each protein sequence in the entry. Selecting one Pfam architecture will return all homodimeric interface clusters of the architecture, as well as heterodimeric interfaces for those chains with different sequences but same Pfam architecture. Selecting two Pfam architecture will return all heterodimeric interface clusters of those two Pfam architectures.  

  For instance, inputing PDB ID "2GTP" will return a table with the Pfam architecture of each sequence, (G-alpha) for entity 1, (RGS) for entity 2 .

  

  Selecting (G-alpha) will return the homodimeric interface clusters of (G-alpha). The title of the table indicates the summary information about the (G-alpha) group. There are 22 crystal forms and 44 PDB entries in the group. The cluster 1 common interface occurs in 6 crystal form and 17 entries, but is not present in any of the PDB and PISA Biological units for these entries. However, the surface area is relatively small (396 sq. Ång) and this interface may not be biologically relevant.

  

  Selecting two Pfam chain architectures returns the heterodimeric interface clusters. The Cluster 1 heterodimeric interface occurs in all 7 crystal forms and all 9 PDB entries that contain these two architectures. The minimum, sequence identity is 50.4% and the average surface area is 834 sq. Å. It is present in all 9 PDB biological units but only 1 PISA biological assembly contains this interface. Hit the “+” sign to see the expanded table, which gives more details about the cluster: the crystal form information, PDB codes, whether the common interface is in the PDB and PISA biological units for each entry, the PDB/PISA biological units in PQS format, the surface area, protein name and species. Collapse the table by clicking the "[-]" in the first column. To download the interface files of each cluster, right-click the cluster id. Download all interface files for the clusters in the group by clicking the button "Download All Cluster Interface Files" at the bottom of the page. All cluster information in a text file can be downloaded by clicking the button "Save Cluster Data". The text file is tab delimited, and can be opened in Excel or other spreadsheet programs.

  

• Pfam ID

  Input one Pfam ID or Pfam accession code to find all PDB entries containing the Pfam. Since not all Pfam are in PDB, you can look through lists of those Pfam that are in the PDB using the Browse button at the top of each page.

• Sequence(s)

  You can input one or two sequences. ProtCID assigns Pfams to the query sequence(s) using the results of the web service provide by Pfam, then shows the likely Pfam domains in a table. If two sequences are input, two tables are returned. Click the button "View Pfam Arch in PDB" to display the table of all entry architectures that are in the PDB that contain one or more of the Pfam domains in the query. If two sequences are input, the table contains pair architectures that contain at least one Pfam domain of the first sequence and one Pfam domain of the second sequence.

  As an example, input a HIV integrase sequence:

  PRGLGPLQIWQTDFTLEPRMAPRSWLAVTVDTASSAIVVTQHGRVTSVAAQHHWATAIAVLGRPKAIKTDNGSCFTSKSTREWLARWGIAHTTGIPGNSQGQAMVERANRLLKDKIRVLAEGDGFMKRIPTSKQGELLAKAMYALNHFERGENTKTNL

  the image below shows the result page:

  

  Click the button "View Pfam Arch in PDB", and a table appears that lists the Pfam architectures of all entries that contain the Pfam and the number of PDB entries for each:

  

  Click one of the Pfam architectures, for instance "rve", and the interface clusters are returned. The common interface in cluster 1 is present in all 11 crystal forms and 39 entries:

  

  Expanding the table with the "[+]" button shows that the interface occurs in 4 different entry architectures. The Pfam architecture of 1C6V is (integrase);(rve), 2B4J is (LEDGF);(rve) and 1BI4 have two chains with same family. 7 PDB biological units and 12 PISA biological assemblies are missing this interface.