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Figure 3 | BMC Bioinformatics

Figure 3

From: Characterization of the cofactor-binding site in the SPOUT-fold methyltransferases by computational docking of S-adenosylmethionine to three crystal structures

Figure 3

20 best docking solutions obtained during the refined (local) docking procedure, mapped onto the surface of the SPOUT superfamily members (monomers) colored by sequence conservation. The protein surface is colored according to the relative sequence conservation among its orthologs (blue – strongly conserved, to cyan – moderately conserved, to red – variable). The orthologous sets for each of the three structures are non-overlapping. a) 1gz0 (53 orthologous sequences), b) 1ipa (54 sequences), c) 1k3r (30 sequences). d) the SPOUT domain of 1gz0, colored by sequence conservation computed for all the three aligned families. Notably, when all three families are considered, the invariant and nearly-invariant residues disappear from the predicted target-binding groove, while a few of them still remain in the cofactor-binding groove (including Gly predicted to interact directly with AdoMet). The invariant side chain at the "bottom" of each monomer comes from the Arg residue, which interacts with the "barrier" structure of the second monomer in the dimer (shown in detail in Figure 4).

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