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Figure 6: VAST structural alignment of 1B8GA3, 3TATA2, and 1DJUA3. The backbone atoms of the
aligned residues of the three structures are shown. The bound pyridoxal phosphate ligands (center) are
shown in a lighter shade of grey.
Appendix 3: Example query: finding and viewing CDs in a protein
Finding CDs in a Protein. Suppose that we are interested in topoisomerase enzymes and
would like to find human topoisomerases that most closely resemble those found in
eubacteria and thus may share a common ancestor. Further suppose that through a
colleague, we are aware of a recent and particularly interesting crystal structure of a
topoisomerase from Escherichia coli with PDB code 1I7D. How can we identify the
conserved functional domains in this protein and then find human proteins with the same
domains? From the Structure main page, we enter the PDB code 1I7D in the Structure
Summary search box and quickly find the Structure Summary page for this record. We
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