The Thalidomide-Binding Domain of Cereblon Defines the CULT Domain Family and Is a New Member of the β-Tent Fold
Figure 9
Structural gallery of aromatic cage-like conformations and associated ligands.
Aromatic residues forming cage-like conformations are depicted in gray, ligands in cyan. Oxygen: red; nitrogen: blue; sulphur: yellow. Panels b–h show examples from the five main categories (S2 Table); their PDB accession codes are shown at the bottom-right corner of each panel. Cage residues are labeled in red by their three-letter names and residue numbers from the PDB entry. Ligands are marked by their three-letter identifiers taken from PDB. (a) Geometric criteria for detecting aromatic cage-like conformations (see Method section for a detailed description). (b) Heterocyclic ring (uracil) bound to the pyrimidine-sensing transcriptional regulator RutR. (c) Hydrocarbon ring (tyrosine) bound to the periplasmic leucine-binding protein of E. coli. (d) Hydrocarbon chain (leucine) bound to the same binding site (1a99). (e) Hydrocarbon chain containing N/O/S (putrescine) bound to the periplasmic putrescine-binding protein of E. coli. (f) Hydrocarbon ring (2-(cyclohexylamino)benzoic acid) bound to the phenazine biosynthesis protein PhzA/B from Burkholderia cepacia R18194. (g) Ammonium cation (metyllysine 9 of histone H3) bound to the Drosophila HP1 chromodomain. (h) Ammonium cation (dimethylarginine) bound to the Tudor domain of human TDRD3.