Using CHIME to clarify the interaction of vancomycin with a target in vitro
The molecular strcuture above is generated from the Protein Data Bank file 1VAN. It ontains in addition to vancomycin itself, a model target molecule L-LYSINE-D-ALANINE-D-ALANINE.
To clarify the identities of the different components of the vancomycin complex, they can be separately coloured, and displayed in wireframe.
In this view, the target (L-LYS-D-ALA-D-ALA) is coloured cyan (light blue). The target is a relatively straight structure, and lies grasped in the middle of the vancomycin molecule, with only the lysine side chain extending away from the complex. The active part of vancomycin is coloured by the CPK convention, while the sugars are coloured purple.
Click here to highlight vancomycin itself by rendering its atoms in dotted surface
Click here to highlight the target by rendering its atoms in dotted surface
The intimate asociation of vancomycin and its target can be clearly seen in a spacefilling view of vancomycin. The target is shown in cyan.
Click here to see vancomycin on its own
Click here to see L-LYS-D-ALA-D-ALA.
If you find that the image becomes confused, you can reset the image to the wireframe state by clicking here.