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Fig. 4 | BMC Biology

Fig. 4

From: Molecular insights into substrate recognition and catalytic mechanism of the chaperone and FKBP peptidyl-prolyl isomerase SlyD

Fig. 4

Binding of peptides to the insert-in-flap (IF) domain. a The substrate-free IF domain of TtSlyDFL:FK506 (molecule B) is depicted as in Fig. 2, except that the backbone of β8 is shown in sticks, and the side chains of residues forming a hydrophobic binding groove are shown in green sticks and semi-transparent spheres. b Binding of the S2 peptide to the IF domain of molecule A in the TtSlyDFL:S2 structure. The backbone of the peptide is shown in pink sticks, and the hydrophobic side chains that are sequestered in the hydrophobic binding groove are shown in sticks and semi-transparent spheres. Dashes indicate main chain hydrogen bonds between the peptide and β8. c Peptide binding in TtSlyDFL:S2 (molecule B). d Peptide binding in TtSlyDFL:S2-W23A (molecule C). e Peptide binding in TtSlyDFL:S2-plus2. f Peptide binding in TtSlyDFL:T1. Additional file 4 shows the electron density map for the S2 peptides bound to the IF domain, Additional file 5 shows an analysis of the structural changes in the IF domain induced by substrate binding, and Additional file 6 shows the peripheral substrate:IF domain interactions

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