Figure 2
From: A unique peptide deformylase platform to rationally design and challenge novel active compounds
SaPDF substrate binding site.
(a) Tripeptide Met-Ala-Ser bound to SaPDF between N- and C-terminal sub-domains is shown in sticks format and colored in yellow, with O in red, N in blue, and S in yellow. α and 310 helices of protein are in pink, β strands in green and insertions in light blue. The three consensus motifs I, II and III are colored in light orange. (b) The network of interactions of the ligand binding site of Met-Ala-Ser in SaPDF is represented: the free amine group coordinates the catalytic metal (Me) and is hydrogen bonded to Glu175; the side chain of Met fits into a hydrophobic pocket called S1’, made of residues Val71, Leu125, Glu129, Tyr167, Val171, His174; the backbone of peptide is hydrogen bonded to Val71, Gly69 and Gly130 of SaPDF. Dotted lines represent the hydrogen bonds. (c) The solvent-accessible surface of S1’ pocket is represented, in apo SaPDF (top) and in the complex with Met-Ala-Ser (bottom). (d) Close-up view of hydrogen bonds that link the backbone of Met-Ala-Ser with residues Val71, Gly69 and Gly130 of SaPDF, linking strands β1 and β4. The color code of panel a is used.
