iCn3D Intro Tutorial C: Finding Pockets in Proteins

Small molecules that bind to larger proteins must have shape AND charge complementarity with the binding pocket in the protein.  You can put a small molecule into an appropriate-sized pocket in a protein.  You can’t put a positively charged small molecule into a pocket lined with a positive charge.  Let’s find the pockets in a small protein, LMWPTP, a phosphatase that cleaves a negatively charged phosphate group (PO₃^-2) proteins (pdb 1xww).  It also binds the small sulfate ion (SO₄^-2) in the same pocket.  

Finding Pockets

Let’s find the pocket where the ligand could bind using a free program called CavityPlus. 2022

1.      Load http://www.pkumdl.cn:8000/cavityplus/computation.php#/ and select Start Computing

2.      Input 1xww, then select Click to Search. Wait until the structure loads to continue. 

3.      Then simply choose Submit.  (Make sure that Use Ligand Mode is not selected)

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4.      After the run, you will see a new window open on the left-hand-side with the protein and the top #1 Cavity  highlighted.  Site 1 is the presumptive location for the binding of SO₄^2-. Use your mouse to rotate the protein to better see the cavity.  To see a list of the amino acids lining the binding pocket surface, and the surface area and volume of the cavity, select … under More. They will appear in the Residue row. 

 

 

5.  Copy and Paste into the table below the list of amino acids comprising the pocket into the table below. Then take a screen snip as shown in the image to the right (Note:  if you can unzip the downloaded file, you could select the Download Results link and use other programs to view the results). 

 

 

Amino acids in pocket	Image snip

 

 

 

Viewing  Small Molecule in a Binding Pocket

Now let’s model the phosphate (PO₃^-2)/sulfate (SO₄^-2) binding site in the phosphatase using iCn3D.   

1.  load 1XWW in iCn3D

2.  Render the proteins as follows:

• Analyses, Sequences and annotation, Details Tab, uncheck conserved domain
• Click 1XWW_A 1^st, then in the top menu bar choose Select, Save Selection and name it phosphatase

• Color, Charge
• Style, Surface Opacity, Fast Transparency, 3
• Style, surface type, molecular Surface

 

 

3.  Next render the SO4 as follows:

• Choose SO4 (2) with the mouse, then Select, Save Selection and name it SO4
• Style, Chemicals, Sphere

 

4.  Snip and paste an image of the protein with the surface display and the bound SO₄^-2 in spheres.

 

 

 

 

5.  Optional: To see actual interactions between SO₄^-2 and the protein

• Style, Remove surface
• Analysis, Interactions,
•  In popup window, choose for 1^st set – sulfate; choose for the 2^nd set – phosphatase; click 3D Display Interactions; Snip table with types/colors on interactions
• View Selection; Style, Sidechains, Stick; Color, by Atom,
• Analysis, Label, Per Residue and number; Analysis, Label Scale, 2;
• Style, background, white
• Snip an image of the interaction legend and modeled interactions, and paste below.