Ligand search tutorial¶

This tutorial aims to give you some hands-on experience of finding protein structures on the PDBe website and viewing them in 3D. Bold text in the tutorial means you need to do something.

Go to: PDBe.org

You should see the following header bar:
Your search begins with the search bar at the top right. Type “acetylcholine” into this bar.
This generates autocomplete results, grouped into different fields. The number next to each name tells you how many PDB entries contain it.

These fields enable you to search for specific information in the PDB. Click on the ‘Acetylcholinesterase’ term in the ‘Enzyme’ autocomplete.
This will return you results for all PDB structures that contain an enzyme classified to be an acetylcholinesterase.

Acetylcholinesterase is an enzyme that breaks down acetylcholine, a molecule which transmits nerve signals to muscles and within the brain. The chemical weapon sarin targets this enzyme, as do certain anti-dementia drugs and snake venoms.

In your search results ,there are a number things you can explore for each ‘hit’, including the following, highlighted in the next image:
- View the PDB entry page for that structure
- View the structure in Mol*, our 3D visualisation software
- Download files related to the entry, e.g. archive files, validation report, experimental data etc.

For the purpose of this tutorial, we will look at a specific example entry:
- Go to entry 1qti by typing “PDBe.org/1qti” into your browser
This takes you to the entry page for a specific acetylcholine structure.
You should see the page displayed below:

Viewing the structure in 3D¶

The first thing we will do is view the structure in 3D using Mol*
click 3D Visualisation highlighted in the red box above
There are a number of options on the right-hand side of the viewer to change how you visualise the structure (highlighted in the image below)

There are three different parts of the structure which you can change the look of the display.
- Polymer – this includes any polymeric molecules, such as proteins and DNA. What ‘type’ of representation this set to by default?
  
  Answer
  Cartoon
  Why do you think that is?
  
  Answer
  Much clearer for displaying large molecules.
- HET Groups – This includes any other molecules which are not part of a polymer (drugs, ions etc). Usually these are much smaller than the polymers. We colour these by element by default – can you work out which atoms form the molecule in that structure?
  
  Answer
  Carbon, Oxygen, Nitrogen
- Water – Most PDB structures contain water molecules as proteins prefer to be hydrated. Therefore, individual water molecules are also found in the structure.
These three types of molecule all have options to view them in different ways. Have a go playing with the options and try the following tasks.
- Show the polymer as ball-and-sticks and set the polymer colouring to element symbol. This is how the chemistry of small molecules is generally represented. Why do you think that we don’t usually display protein structures this way?
  
  Answer
  It is too complicated to see what is going on.
- Show the polymer as a surface and the HET groups as ball-and-sticks. Scroll the mouse wheel down to cut away the view of the protein. Can you see the small molecule in the binding pocket?
- Show the polymer as cartoon and set the polymer colouring to ‘Rainbow (chain).’ Can you trace the protein chain all the way from the beginning (dark blue) to the end (red)?

Viewing small molecules bound to proteins¶

Return to the entry page for 1qti
- Either close the Mol viewer or go to PDBe.org/1qti.*
The small molecules in the PDB entry are displayed in the ‘Ligands and Environments’ section (in the red box below). This structure is galanthamine, an Alzheimer’s drug found in Snowdrops.

How many bound small molecules are there in the entry?

Answer
1.
Next we will go the ligands page for that specific small molecule.
- Click on the image of the small molecule or three letter code.
The grey banner at the top of the page gives you some information about the molecule.
- This includes the chemical formula of the molecule and its molecular weight in Daltons. What is the molecular mass of galanthamine?
  
  Answer
  287 Daltons
There are also images of the small molecule at the top right.
Next, turn your attention to the ‘Environment details’ section further down the page, where there are two sections:
- On the left is an image displaying the small molecule and all of the amino acids that form the binding site for this molecule.
- On the right is the Mol* viewer, displaying in the same data in 3D. The experimental data (electron density) is also shown.
The image on the left displays the bound small molecule in purple, in ball-and-sticks representation. The amino acids in the binding site are shown in two different ways:
- Polar Interactions: Amino acids interacting this way (eg hydrogen bonding) are shown in Ball-and-sticks representation, coloured orange. Can you identify which amino acids form hydrogens bonds with the ligand and how long these hydrogen bonds are (Note: the hydrogen atoms are not shown)? Do these distances correlate with what you would expect for hydrogen bond lengths?
  
  Answer
  Ser200 (2.97 Angstrom) and Glu199 (2.72 Å) – these are about right.
- Hydrophobic interactions. Amino acids interacting in this way are shown as a dashed arc, coloured red. How many amino acids IN TOTAL form the binding pocket?
  
  Answer
  12 (including Ser200/Glu199).
Try interacting with the Mol* viewer on the right. It shows the electron density that the molecule was fitted into. How well do the atoms fit into the mesh? Do you think the molecular modelling is reliable?

Answer
These fit pretty well which would suggest reliable modelling.