Crystal structure of retinol-binding protein 4 (RBP4) in complex with non-retinoid ligand A1120 and engineered binding scaffold

Structure

x-ray diffraction · 2 distinct chains · 12% helix, 45% strand (DSSP).

Ligands and binding sites

• 2T1 · 2-[({4-[2-(trifluoromethyl)phenyl]piperidin-1-yl}carbonyl)amino]benzoic acid · ligand · chains A, B
• ZN · Zinc ion · metal · 3 copies · chains A
• IMD · Imidazole · additive · 5 copies · chains A
• PEG · Di(hydroxyethyl)ether · additive · chains A
• ACT · Acetate ion · additive · chains B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 859 Ų buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

• 6QBA · Crystal Structure of Retinol-Binding Protein 4 (RBP4) in complex with non-retinoid ligand… · the same entry in another collection · chain A against A, TM-score 1.00
• P02753 · AlphaFold monomer V2.0 prediction for retinol-binding protein 4 (P02753) · a predicted model of the same protein · chain A against A, TM-score 0.97
• P61991 · AlphaFold monomer V2.0 prediction for DNA-binding protein 7A (P61991) · a predicted model of the same protein · chain B against A, TM-score 0.74

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
• Every structure of UniProt P61991
• Elsewhere: RCSB PDB 6QBA · PDBe 6QBA · UniProt P02753 · UniProt P61991