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Proteins:
Informatics
Assignment
A. Read the following articles
Berman 2004 The Impact of Structural genomics on the Protein
Data Bank
Murzin 1995 SCOP
B. Provide written answers to the following
questions,
to be turned in prior to the Wed class, as per these instructions.
- What is Structural Genomics?
- What is the Protein Data Bank (PDB), and how are new structures entered into the database?
- How are proteins classified in SCOP?
- One of the reactions in the TCA cycle is oxaloacetate plus
acetyle-CoA to citrate. Search the EcoCyc pathway database
to find this reaction, and show a screenshot of it.
- One of the enzymes involved in this reaction is citrate synthase.
Click on the citrate synthase enzyme on the Ecocyc page showing the
reaction, and note the five PDB entries for this enzyme. Click on
the first one to go to the PDB. Provide the PDB identifier of
this protein, and show a screenshot of its molecular structure
using any of the molecular viewing tools at the PDB site.
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