Download (http://www.pdbe.org) To appreciate the structural features and

To appreciate the structural features and complexity of proteins, it’s best to view them in 3D and
manipulate the structures yourself. Using PyMol, you can explore the different structural features
you’ve learned about, for every protein you could think of. Follow the instructions shown in bold blue.
Use the PDB Loader Service to
load up ubiquitin (1ubq).
Plugin > PDB Loader Service
To find out about ubiquitin,
look it up on the PDBE website.
(http://www.pdbe.org)
Hide everything as shown in
the screen shot.
H > Everything
You can choose to show the
protein as lines, sticks or
ribbons (make sure to ‘Hide
everything’
before
you
change between views).
Choose to show the
protein as a cartoon.
S > Cartoon
Next, click the ‘S’ at the bottom of the
screen. This will allow you to see the
sequence of amino acid residues which make
up the primary structure of your chosen
protein.
This gives you a good idea of
the secondary structural
features (α-helices, β-sheets)
in the protein and makes it
easier to manipulate.
The amino acid sequence is shown at the top
of the screen using their one-letter codes.
You can use your mouse to highlight
particular amino acid residues to see where
they are in the protein.
Alternatively, you can colour the protein by
secondary structural feature (C > by ss) as
shown below. α helices, β sheets and loops are
shown in different colours. You can also see
which amino acid residues make up which part
of the protein.
To see the individual
amino acid residues
and their R-groups,
choose to display the
side chains.
S > side chain > lines
To view the hydrogen
bonds responsible for
keeping the secondary
structures in place,
display
the
polar
contacts.
Explore some more features of PyMol until you feel
comfortable with how it works and the features that
are available to help you understand and visualise
protein structure.
A > find > polar
contacts > just intramain chain
Produced by Lucy Jakubecz at Newcastle University as part of an MChem project.