Bioinformatics: Phosphoglycerate Kinase Lab, science assignment help

Visit: http://blaster.docking.org/query.shtml

Enter 95201 –> Select “Query Job”

Using Chimera or Pmol :

1) produce an image of phosphoglycerate kinase overall 3D structure in cartoon format with ligand in specify CPK

2) produce an image of phosphoglycerate kinase showing active site with inhibitor(ligand) bound (active site isolated in stick format with ligand in ball-and-stick)

If you return to the results page, there is a section that reads “Large Database docking results available”. Select Browse “Subset 12”. Identify the rank 1 compound (This is the top inhibitor of phosphoglycerate kinase). Calculate it’s kd. Compare calculated kd to that of other binding reactions (Especially to that of Avidin and biotin). 

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