Sandbox 323

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You may include any references to papers as in: the use of JSmol in Proteopedia ^[1] or to the article describing Jmol ^[2] to the rescue.

The discovery and characterization of the structure and function of the protein 3ds8.

The purpose of this project was to characterize the function of an unknown protein 3ds8 with known structure by comparing it to known proteins and subjecting it to different tests in the laboratory. Different techniques to achieve this goal include protein expression, purification and analysis, kinetics, and computational methods.

Function

Experimental

The beginning experiments were conducted on molecular docking sites to compare the structure of the 3ds8 active site with known proteins. Using the SPRITE database [1], the 3ds8 protein was matched with a few proteases through right-handed superpositions with RMSD values ranging from 1.20-1.40, indicating relative similarities. The left-handed superpositions matched with more trypsins and displayed better RMSD values ranging from 0.93-1.11.

Relevance

Structural highlights

This is a sample scene created with SAT to by Group, and another to make of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.