Nest (protein structural motif)

[1][2][3][4][5][6][7][8][9] Each consists of the main chain atoms of three consecutive amino acid residues.

The conformation of a nest is such that the NH groups of the first and third amino acid residues are liable to be hydrogen bonded to a negatively charged, or partially negatively charged, atom, often an oxygen atom.

Another occurs at the bottom of a deep cavity in the antibiotic peptide vancomycin which binds a key carboxylate group utilized during the final stages of bacterial cell wall synthesis, thereby preventing bacterial cells from multiplying.

Because their concavities are often wider than simple nests, compound nests are commonly employed by proteins for binding multi-atom anions such as phosphates, as in the P-loop or Walker motifs, and in iron-sulphur clusters.

A number of antibody proteins have RLR nests within the hairpin loops of their H-chain CDRs (complementarity determining regions) bound to a carboxylate side chain.

These have been engineered to give rise to monoclonal nest-containing antibodies specific for proteins with phosphorylated serines and threonines.