PDB file 1PDA
This file depicts activated Porphobilinogen Deaminase from E. coli, with bound prosthetic group dipyrromethane. The structure was solved by G. V. Louie et al., in 1992.
Suggested display options:
Select protein and display
as cartoon with color
Note how the protein is organized as 3 approximately equivalent domains.
Select ligand, display as sticks,
and color CPK, to visualize the
Note its position at the junction of the three protein domains.
The dipyrromethane cofactor is covalently linked to the enzyme by a
thioether bond to the sulfur atom of a cysteine side-chain.
Select cys242 and display as ball & stick with color CPK to view the linkage.
To confirm the covalent bond, try also displaying the ligand and cys242 in spacefill.
Try also selecting protein and display as spacefill
with color chain.
Question: Does there appear to be room in the active site cleft for four more pyrrole rings?
How might extra space be provided? (Try going back to protein display cartoon.)
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