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Figure 2 | BMC Bioinformatics

Figure 2

From: Variation in structural location and amino acid conservation of functional sites in protein domain families

Figure 2

Interaction profile of the RICIN domain. Alignment of positions corresponding to an HMM match state. Sites interacting with saccharides are indicated in blue, peptide interactions in orange, and sites interacting with both ligands, saccharides and peptides, are indicated in purple. Light colours represent backbone interactions, darker colours involve side chain atoms. The amino acid conservation is visualized by green bars below the alignment. Sugar binding sites described in the literature are indicated by red arrows above the alignment [41]. Several positions (1, 3, 4, 22, 42, 58, 88, 90, 122) are located in the vicinity of a glycosylation site, but do not specifically interact with saccharides. The unrooted tree reflects the classification into three main subgroups with different interaction sites. Group II harbours two sugar-binding sites, group I and III originate from tandem RICIN domains, in which group I preserved the N-terminal sugar-binding site and group III the carboxy-terminal binding site. PDB identifiers from top to bottom: 1PC8 (B: 5–131), 1TFM (B: 5–131), 2MLL (B: 5–131), 1CE7 (B: 5–131), 1ONK (B: 9–135), 1PUM (B: 9–135), 1M2T (B: 257–383), 1OQL (B:13–139), 1ABR (B: 13–139), 2AAI (B: 8–134), 1HWO (B: 10–135), 1HWP (B: 10–135), 1HWN (B:10–135), 1HWM (B:3–266), 1V6U (A: 312–436), 1ISW (A:312–436), 1ISV (A:312–436), 1ITO (A:312–436), 1V6W (A: 312–436), 1V6X (A: 312–436), 1XYF (A:312–436), 1ISY (A: 312–436), 1ISZ (A:312–436), 1V6V (A:312–436), 1ISX (A:312–436), 1KNM (A:7–131), 1KNL (A:9–133), 1BFM1MC9(A:9–133), 1QXM (A: 29–157), 1PUM (B: 140–262), 1M2T (B: 390–510), 1ONK (B: 140–262), 1OQL (B: 140–262), 1PC8 (B: 136–254), 1TFM (B: 136–254), 2MLL (B: 136–254), 1CE7 (B:136–254), 2AAI (B: 138–261), 1ABR (B: 143–266), 1HWO (B: 138–262), 1HWP (B: 138–262), 1HWM (B: 138–262), 1HWN (B: 139–263), 1FWU (A: 3–123), 1DQG (A: 4–124), 1DQO (A: 4–124), 1FWV (A: 3–123)

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