Use the form below to search the database. You can search on characteristics of the Protein, DNA, DNA-Protein Interface, Nucleotide-Residue Interactions or any combination of these. You can also search directly for specific PDB entries, or enter a list of PDB IDs and additional criteria to select a subset of structures from the supplied list of IDs. When using the form, blank or empty fields will be ignored, so If you don't care about a particular feature then feel free ignore it. Some examples are provided below - for a detailed explanation of how to use the database and the format of the returned data, see the documentation.
The following are a few examples which show how to search the database in different ways. Click on any of them to see step-by-step instructions. For a full explanation of searching, see the documentation page.
In this example, let's construct a search which uses DNA Properties and DNA-Protein Interactions to find TATA binding proteins (TBP) in the database. TBPs bind to the core sequence TATAAW, where W is A or T (see IUPAC DNA codes), and are unusual in that they bind in the minor groove via one or more beta sheets. To accommodate the binding domain, the minor groove must open up, which effective bends and unwinds the DNA, greatly distorting it from a typical B-DNA conformation.
First choose the DNA Properties option from the criteria selection box.
Now, let's enter the TATA box motif by filling in "TATAAW" in the "Contains Seq. Motif" field, and check the "search within binding site" box to ensure that the protein is actually bound to that sequence (i.e. exclude the flanking sequences of the binding site from the search). Next, check "A-DNA" and "other" in the "DNA Conformation" options. This will exclude B-DNA from the search, since TBPs distort their target binding site.
Next, let's add an DNA-Protein Interaction criteria. After the DNA Properties selections are chosen, click the "add another criteria" button. This will append a new criteria selection box beneath the DNA-Properties pane.
Choose Protein-DNA Interactions, and click on the "Minor Groove Contacts" selection. Choose "strand". This will ensure that all matching structures contain strands bound in the minor groove. Note that this does not exclude the possibility that some matching structures contain helices or loops in the minor groove, however, our search will be specific enough as is. Leave the rest of the options under DNA-Protein Interactions blank.
Finally, click the "search" button at the bottom of the form, and make sure that the "Match on" option is set to "ALL".
A new window will open and you will be presented with a table of matching structures. This search returned 15 structures, and a quick inspection of the "Protein Name(s)" column confirms that we indeed have a list of TATA binding proteins.