Graphics Gallery
Gale Rhodes
Chemistry Department
University of Southern Maine
Revised 2006/08/02
Learn how to use Swiss-PdbViewer. Work through sections 1-4 of
the Swiss-PdbViewer
Tutorial.
Topic: Amino-Acid Metabolism
Examples:
Featuring cofactors studied in this section of the course.
Aspartate Aminotransferase, complex with PLP (PDB file codes 8AAT
and 9AAT)
This enzyme catalyzes transaminase reactions involving
oxaloacetate as nitrogen acceptor.
From the Protein Data Bank, download files 8AAT
and 9AAT.
The model in file 8AAT contains pyridoxal phosphate joined as an
aldimine to the active-site lysine. The model in file 9AAT contains
pyridoxamine in the active site.
- Use SwissPdbViewer to compare these structures. They should be
superimposed when loaded; if not, use Fit: Magic Fit to
superimpose them.
- To examine cofactor binding, display groups within 5 angstroms
of PLP, which is the last group listed in chain A.
- What are the differences between the nature of PLP binding in
this enzyme and in glycogen
phosphorylase?How do these differences pertain to the
different functions of PLP in aminotransferases and in
phosphorolysis of glycogen?
Topics List
Biochemistry
Resources