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Sandbox GGC13

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<scene name='78/781197/Oxamate/3'>Close up interactions between the substrate binding pocket and the inhibitor, oxamate. The substrate active site to which oxamate is bound is in the closed conformation.</scene>
<scene name='78/781197/Oxamate/3'>Close up interactions between the substrate binding pocket and the inhibitor, oxamate. The substrate active site to which oxamate is bound is in the closed conformation.</scene>
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<scene name='78/781197/Nadh/1'>Close up interactions between the NADH and adenine binding pockets and the cofactor, NADH.</scene>
 
The nicotinamide and adenine binding pockets work together to sufficiently bind NADH. Both binding pockets implement hydrogen bonding and hydrophobic interactions with their ligand fragment. In addition to the interactions within the binding pockets, NADH is also supported by ionic forces between arginine (R99) and the pyrophosphate groups.
The nicotinamide and adenine binding pockets work together to sufficiently bind NADH. Both binding pockets implement hydrogen bonding and hydrophobic interactions with their ligand fragment. In addition to the interactions within the binding pockets, NADH is also supported by ionic forces between arginine (R99) and the pyrophosphate groups.
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<scene name='78/781197/Close up interactions between the inhibitor, oxamate and the cofactor, NADH./1'></scene>
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<scene name='78/781197/Nadh/1'>Close up interactions between the NADH and adenine binding pockets and the cofactor, NADH.</scene>
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The hydroxyl groups of NADH's ribose fragments interacts with the H-bond network created by the substrate and asparagine (N137).
The hydroxyl groups of NADH's ribose fragments interacts with the H-bond network created by the substrate and asparagine (N137).

Revision as of 01:04, 22 April 2018

Crystal Structure of Lactate Dehydrogenase A

Crystal Structure L-Lactate Dehydrogenase A interacting with inhibitor, Oxamate

Drag the structure with the mouse to rotate

References

  1. ↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
  2. ↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644
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