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. 2004 Apr 28;339(3):607–633. doi: 10.1016/j.jmb.2004.04.012

Figure 9.

Figure 9

(a) Recognized similarity (ranked 19) of an ADP-binding site of a replication factor C (1iqp, colored purple) to the adenine-binding site of cAMP-dependent protein kinase (1atp, colored cyan). The Figure presents the obtained superimposition of the ligand molecules as well as of the functional groups. The functional groups that are shared by these sites are represented as spheres colored according to their physico-chemical properties as in Figure 2 (the spheres of 1atp are larger). (b) Recognized similarity (ranked 31) of functional groups and the alignment of ligands of an ADP-binding site of d-Ala-d-Ala ligase (1iow) to the adenine-binding site of cAMP-dependent protein kinase (1atp). (c) Recognized similarity (ranked 38) of the estradiol-binding sites of estrogen sulfotransferase (1aqu, blue) and sex hormone-binding globulin (1lhu, yellow). The estradiol ligand of 1lhu is cyan and that of 1aqu is purple. (d) Recognized similarity (ranked 43) of a binding site of a tropinone reductase (2ae2) to an estradiol-binding site of sex hormone-binding globulin (1lhu, depicted as cyan dots). The estradiol ligand of 1lhu is purple and an estradiol molecule that is placed in the binding site of 2ae2 according to its structural homologue (1fds) is shown in green. The two binding sites are recognized to share three residues that have the same spatial location and identity of the amino acid. The residues of 2ae2 are blue and those of 1lhu are red. (e) A false-positive solution that recognizes a similarity of the adenine-binding site cAMP-dependent protein kinase to a region of photosynthetic reaction centre (1dxr). The ATP molecule of 1atp is green. The surfaces of the two binding sites are depicted as dots (1atp, red; 1dxr, blue) and the functional groups are depicted as spheres. (f) A presumably false-positive solution of similarity of a CXE-binding site of an outer membrane protein NspA (1p4t) to an estradiol-binding site of sex hormone-binding globulin (1lhu). The binding sites are depicted as dots (1lhu, red; lp4t, blue) and the ligands as sticks (1lhu, green; 1p4t, purple).