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Fig. 5 | BMC Genomics

Fig. 5

From: Marsupials and monotremes possess a novel family of MHC class I genes that is lost from the eutherian lineage

Fig. 5

Predicted structure of UT proteins. a Sequence alignment of the α1 and α2 domains of UT4, 5, 6, 8 with 7 of the top 10 structural analogs from Protein Data Bank (PDB) identified by I-TASSER. Orange bars show α-helices. Green arrows highlight β-strands. Major differences between the UTs and templates are indicated by arrows, or red lines, and the consequence of these on the protein structures are shown in Fig. 5c. b Overlay of the backbone of the peptide binding groove of mdUT4 with its top 2 structural analogs, 3BEV_A (ggB21) and 3P73_A (ggYF1). c Superposed model structures of mdUT4, 5 and 8 with the B21 template shows the antigen-binding groove is open, but possibly short. Filled sphere view shows the α-helices and ribbons show the β-sheets of the peptide-binding platform on the modeled protein structures. The residues indicated with arrows in Fig. 5a cause the binding grooves to be short or narrow (e.g. UT4: the distance between Pro81 Cγ to Tyr144 OH is 3.0 Å; UT5: the distance between Pro81 Cβ to Tyr144 OH is 2.9 Å, and a close hydrophobic contact between 64 LTQW 67 and 161 MNLY 154 ; UT8: the distance between Phe75 Cε to Phe138 Cξ is 2.9 Å)

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