Download Aim: To navigate the PDBe website and interpret the given

Aim: To navigate the PDBe website and interpret the given information about a specific protein.
The sodium-potassium pump is found in cellular membranes – its main job is to generate an ion gradient
by pumping sodium ions out of the cell, and potassium ions in. To do this it gets energy from ATP. As
more and more sodium leaves the cell, an electrical gradient and a concentration gradient are created.
These gradients are vital for tasks such as transmitting nerve signals and controlling the osmotic
pressure in cells.
Visit the PDBe homepage (http://www.ebi.ac.uk/pdbe) and load up the summary page for the
sodium-potassium pump (2zxe). Explore the information and answer the questions below.
1. View the protein in 3D using the ‘Visualisation’ tab or loading up the structure into PyMol.
What do you notice about this protein? Describe the key structural features you can see. Do
you notice any ligands?
2. Navigate the different ‘Structure’ links.
a. Primary
How many chains are involved in this protein?
Which is the largest chain?
Which Pfam group does Chain G belong to? (name and code)
b. Secondary
What is the most common structural feature of this protein? What do you know
about this structural feature?
c. Quaternary
Describe the quaternary structure of this protein.
3. Return to the ‘Summary’ page and find the ‘GO’ (gene ontology) information.
a. List the biological processes this protein is involved in.
b. Which chain do you think is the most important to the function of this protein?
Why?
c. List the cellular component for each chain.
Chain A:
Chain B:
Chain G:
4. List the ‘Ligands’ associated with this structure.
5. State the most common ligand (with the most instances in this entry) and state which amino
acid it most commonly binds with.
Produced by Lucy Jakubecz at Newcastle University as part of an MChem project.