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![[Figure 4]](qe5012fig4mag.jpg)
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Figure 4
The UPAR-1109 binding site is shown in ribbon representation. (a) Close-up view of the UPAR-1109 binding site colored as in Fig. 3 ![[link]](../../../../../../logos/arrows/d_arr.gif){kind=small} . The side chains that interact with UPAR-1109 are shown, and hydrogen bonds are shown as dotted lines. In addition, the water molecules that form part of the proton-translocation pathway are labelled W1 and W2. The zones where aliphatic and aromatic amino-acid residues that interact with UPAR-1109 via hydrophobic interactions are concentrated are indicated as S3 and S5, respectively. The polar interaction site involving Asp–Tyr is indicated as S4. (b) Overlay of the UPAR-1109-bound structure (PDB entry 9kbe) and the apo structure (PDB entry 6ajf). The Asp–Tyr pairs, important residues involved in proton translocation, as well as two aromatic residues (Phe260 and Phe649), are highlighted in magenta (PDB entry 9kbe) and cyan (PDB entry 6ajf). The distances between OD1 of Asp and OH of Tyr of each pair are also shown in Å. Ribbons are colored according to the superimposed Cα r.m.s.d. values of the corresponding locations. A scale bar showing the color gradient with the corresponding r.m.s.d. value is shown. |
![[Figure 4]](qe5012fig4.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
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