Figure 5.
SpLdcB with Bound MurNAc—L-Ala—D-γ-Gln—L-Lys—(D-Asn)
(A) Cartoon representation of SpLdcB, drawn using the same color scheme as in Figure 3. The MurNAc—Ala—D-γ-Gln—L-Lys—(D-Asn) is drawn as a ball-and-stick model with Refmac-weighted 2Fobs-Fcalc electron density displayed at a contour level of 1 σ.
(B–E) The interactions made between the ligand and the protein at each subsite are shown successive panels: (B) S3; (C) S2; (D) S1, and (E) S1′. Key van der Waals’ interactions are shown as a transparent silver line.
(F) A schematic of the interactions of SpLdcB with the bound peptidoglycan mimic. Hydrogen-bond interactions are shown with a black dotted line, and van der Waals’ forces are shown with a green arc.
(G) A schematic of the tetrapeptide substrate of SpLdcB, drawn in the same manner as the peptidoglycan mimic in (F). The scissile bond is highlighted by an arrow. Crosslinks to other stem peptides would take place via the lysine’s terminal amino group on the left.