How to use Ligand Explorer - How to use Ligand Explorer...

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How to use Ligand Explorer Since a lot of people were having trouble using Ligand Explorer, I figured I would make a guide explaining how to use it. You can obtain some information for the lab from Cn3d, but actually looking at the active site and doing a lot of the analysis will come from Ligand Explorer. I ll also be doing everything from the perspective of ADH1. If you have any questions, feel free to text me at 949-275-7376. Just make sure you say in your first post that you re from 153L. How to get to Ligand Explorer: All of this info is in the lab manual, but it seems like people don t even know this function exists. So here we go. How to access Ligand Explorer: You re going to need Java for this too. 1. Go to the Cn3D webpage for the protein you want. 2. At the top right corner of the screen is going to be a PDB ID: XXXX. Click XXXX.
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3. On the next page, scroll down until you see Ligand Chemical Component or what is pasted below. 4. Now click the box that says Ligand Explorer next to any of them. It doesn t matter for which molecule. Then just click Launch RCSB Ligand Explorer on the next page!
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General notes: Interactions between cofactors, substrates, etc. and the protein are generally non-covalent interactions: So hydrogen bonds, coordination bonds with metals, and hydrophobic interactions. Only exception is when the protein is undergoing covalent catalysis. So, how does a cofactor interact with the enzyme? H bonds!
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