Uploaded September 2023 | Updated September 2026, 9 hours ago

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In this lesson, KP will show you how to generate a binding site quickly, by creating a selection sphere within a certain number of angstroms from a bound ligand. This lesson focuses on the mouse control menu, and how to use edit mode to reposition labels.

00:00 Intro
00:26 Setting up your workspace
01:57 The mouse control menu
02:34 Selected by distance from a ligand
03:41 Adjusting water sphere size
04:09 Find polar contacts (display binding site interactions)
04:46 Modifying the binding site residue selection
05:50 Show only the amino acid side chains
06:25 Labeling the binding site residues
06:44 Edit mode and moving labels
07:41 Display the binding site without cartoon

REFERENCES
• PDB ID: 6PFK
• Schirmer, T., Evans, P. Structural basis of the allosteric behaviour of phosphofructokinase. Nature 343, 140–145 (1990). doi.org/10.1038/343140a0