Crystal structure of retinol-binding protein 4 (RBP4) in complex with a non-retinoid ligand

Structure

x-ray diffraction · 1 distinct chain · 11% helix, 47% strand (DSSP).

Ligands and binding sites

• 2WL · (1-benzyl-1H-imidazol-4-yl)[4-(2-chlorophenyl)piperazin-1-yl]methanone · ligand · 2 copies · chains B, A
• PO4 · Phosphate ion · ion · 2 copies · chains B, A
• EDO · 1,2-ethanediol · additive · 20 copies · chains B, A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• B–A · 83 Ų buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

• 4PSQ · Crystal Structure of Retinol-Binding Protein 4 (RBP4) in complex with a non-retinoid… · the same entry in another collection · chain B against B, TM-score 1.00
• P02753 · AlphaFold monomer V2.0 prediction for retinol-binding protein 4 (P02753) · a predicted model of the same protein · chain B against A, TM-score 0.96

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt P02753
• Elsewhere: RCSB PDB 4PSQ · PDBe 4PSQ · UniProt P02753