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For this exercise, you need either Pymol or Yasara installed that has the 3DM plugin. If you don't have Yasara or Pymol or you are missing the 3DM functionality, please consult the installation instructions. Before you start this exercise make sure you have the latest version of Yasara or Pymol installed.
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Structures can be loaded directly in Yasara from the 3DM database via the 3DM → Structures → load structure from the 3DM option. Loading structure files via the 3DM menu ensures that the structures are all superimposed, co-crystallized compounds will have to be positioned in the active site and proteins will have the 3D numbering.
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Where do you think the extra OH will be positioned? |
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The OH unique to OAH is sticking right towards ser157. |
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Modeling the extra OH in the active site with the "swap" option does not work very well in yasara, because yasara can't deal with changing the double bond of C=O to the single bond of C-OH without proper EM energy minimization (try to make the diol with the swap option if you like).
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