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Figure 1
(a) Chemical structure of vancomycin. The residue numbering for the amino acids of the glycopeptide is given in gray. (b) Schematic representing the interaction of the D-Ala-D-Ala peptide (black) with the antibiotic (blue). Five key hydrogen bonds that link the peptide to the antibiotic are shown as dashed lines. The red dashed line represents the hydrogen bond that is disrupted during binding of the D-Ala-D-Lac ligand. (c) Structure of the D-Ala-D-Lac ligand; the oxygen atom of the D-lactate is highlighted in red. (d) Structure of the D-Ala-D-Ser ligand; the serine side chain is highlighted in blue. (e) Divergent stereoview of a back-to-back vancomycin dimer bound to D-Ala-D-Ser. The dipeptide ligands are shown in ball-and-stick representation. Color scheme: nitro­gen atoms, blue; oxygen atoms, red; chlorine atoms, green. Carbon atoms are yellow for the ligand, gray for the vancomycin aglycon, cyan for the glucose sugar and orange for the vancosamine sugar. (f) Representative 2Fo − Fc electron density shown for one vancomycin molecule, contoured at 1.6σ. (g) 2Fo − Fc electron density for one D-Ala-D-Ser ligand, contoured at 1.6σ.

IUCrJ
Volume 11| Part 2| March 2024| Pages 133-139
ISSN: 2052-2525
https://doi.org/10.1107/S2052252524000289