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Figure 6 | BMC Bioinformatics

Figure 6

From: Protein structural similarity search by Ramachandran codes

Figure 6

Examples of distantly related proteins retrieved by SARST. (a) The superimposed structures (cross-eye stereo view) of the interleukin 8-like chemokines from human, [SCOP:d1b3aa_] (blue) and [SCOP:d1tvxa_] (red). These two proteins have a low sequence identity while their structures are highly similar. The minimum RMSD calculated from positive positions of the Ramachandran sequence alignment is 1.68 Å. (b) Three-dimensional structures and the superimposition of [SCOP:d1tpo__] (blue) (SCOP sccs id: b.47.1.2), the trypsin from Bos taurus, and [SCOP:d1p3ca_] (red) (SCOP sccs id: b.47.1.1), a Bacillus intermedius glutamyl endopeptidase. These two proteases belong to different families but have similar structures. Although the amino acid sequence alignment fails to detect their functional similarities, the catalytic triad residues (highlighted in green) are well aligned by SARST. Their minimum RMSD is 4.17 Å, whereas their amino acid sequence identity is 22%. The secondary structural cartoons were generated by PROCHECK [54] and then modified with colors and gaps.

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