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Figure 3.
Fig. 3. Substrate binding to OPR1 and OPR3. (a) Stereo view
of the active-site cavity of the OPR1:(9R,13R)-OPDA complex. In
addition to the molecular surfaces of OPR1 (grey; surface of
FMN: green) and of the substrate (9R,13R)-OPDA (yellow), Tyr246
and Tyr78 that narrow the opening of the cavity as well as
(9R,13R)-OPDA are shown as ball-and-stick models (blue). (b)
Stereo view of the active-site cavity of a modeled
OPR3:(9R,13R)-OPDA complex. Surfaces were colored as in (a). The
complex was obtained by transferring the substrate's coordinates
of the aligned OPR1:(9R,13R)-OPDA complex to the OPR3 structure.
Protein residues of OPR3 and the substrate's carboxy alkyl chain
(shortened in the figure for clarity) clash in the model because
OPR3 lacks the tunnel that accommodates the carboxy alkyl chain
in OPR1. In OPR3, these clashes can be easily avoided by a
change in the conformation of atoms C1 to C8 of the carboxy
alkyl chain. In comparison to OPR1, the opening of the OPR3
cavity is lined by His244 and Phe74, resulting in a wider
entrance and leaving more space near the stereo centers of the
substrate.
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