Figure 3.

Overall structure of TtDdl. ATP and d-Ala-d-Ala are shown as ball-and-stick models. (a) Ribbon structural drawing of unliganded TtDdl in the open form. ATP and d-Ala-d-Ala are modelled into the active site by superposing TtDdl–ATP–d-Ala-d-Ala onto unliganded TtDdl. The N-terminal, central and C-terminal domains and loops (loops I, II and III) are shown as yellow, cyan, green and red ribbons, respectively. β-Strands are denoted by β1–β15 and α-­helices by α1–α10. The N- and C-termini are labelled. (b) Superposed backbone structures. The molecular structures of unliganded TtDdl in the open form (grey), TtDdl–ADP in the semi-open form (orange), TtDdl–ADP–d-Ala in the semi-closed form (cyan) and TtDdl–ATP–d-Ala-d-Ala in the closed form (magenta) forms were superimposed by fitting the C^α atoms of the N- and C-terminal domains. The loops are represented by bold lines.