Introduction
This practical will introduce you to the Nucleic Acid Database and two tools for the prediction of conserved motifs in DNA-binding proteins. There are a number of learning outcomes

• Examine protein-DNA complexes stored in the NDB
• Employ the DNA-pred tool to predict the location of HTH motifs in proteins
• Employ the predictdnahth tool to predict the location of HTH motifs in proteins

Practicalities
The links to the database and search tools are shown in the bar on the right side of the page. If you click on any link in this menu you will get a new window in which to view the site.

Data Table
In the table below are 4 protein structures identified by their PDB codes

#	PDB code	Chain ID	File type
1	1gdt	A	Protein-DNA complex
2	1rep	C	Protein-DNA complex
3	3daa	A	Protein
4	1hw5	A	Protein

Practical Tasks

Part A. Search for structures 1gdt & 1rep in the NDB and explore the entries for each.
What form of DNA is bound to these proteins and do they have any additional DNA features?

Part B. Employ the PDNA-pred tool to search for HTH motifs in each of the proteins

1. Download file from PDB (click here for detailed instructions)
2. Upload file to PDNA-pred
   • use the browse bar to locate the file you downloded from the PDB
   • Enter the chain id as indicated in the Data Table above
   • Click on the submit bar ...then wait 1 or 2 minutes for the results

1. Enter the pdbcode in the PDBID box
2. Leave the EMAIL ADDRESS box blank
3. Click on the send bar....

Answers

• Click answers to find out what you should have seen.