Hexokinase PDB id: $2$E$2$P

Ligands: ADP $($Adenosine diphosphate$)$

PDB id: $2$E$2$O

Ligands: Glucose $($BGC$)$

a$)[4$ marks$]$ Using PyMOL and the PDB code for State $1$ of the protein, visualize the protein in

cartoon format with the chains in different colours. The ligands listed for this state in the

table above must be shown in stick format with the atoms coloured by element.

$$ Prepare a figure that clearly shows these features $($i$.$e$.$ the protein bound to the ligand$),$

with a detailed caption that clearly states what it represents.

b$)[6$ marks$]$ Using PyMOL and the PDB code for State $2$ of the protein, visualize the protein$$s

binding site for the ligand$($s$)$ given. Show the protein backbone in cartoon format, and the

ligand in stick format. Identify the residues that form intermolecular interactions with the

ligand, and show them in stick format $[$Hint: You can identify these residues in PyMOL by

selecting those closest to the ligand $($right click, then actions$>$modify$>$around$>$residues

within $4$ A$),$ or by using information from the primary literature $($i$.$e$.$ publications on the

protein$)].$ Use different colours for the carbon atoms of the ligand and the protein residues

surrounding it$.$

$$ Prepare a figure that clearly shows these features $($i$.$e$.$ the binding site with ligand and

the residues that form interactions with it$),$ with a detailed caption that clearly states

what it represents.

c$)[10$ marks$]$ Provide a list of at least five of the interactions identified in $($b$)$ above in table

format, using the example that is provided as template $($note that this example does not

relate to the specific proteins of this assignment in any way!$).$

# Residue

involved

Type of

interaction Atoms$/$groups involved Interaction

distance $($in $)$