1B3H

OLIGO-PEPTIDE BINDING PROTEIN COMPLEXED WITH LYSYL-CYCLOHEXYLALANYL-LYSINE

Summary for 1B3H

• Entry DOI: 10.2210/pdb1b3h/pdb
• Descriptor: PERIPLASMIC OLIGOPEPTIDE-BINDING PROTEIN, LYS-ALC-LYS PEPTIDE, URANIUM ATOM, ... (4 entities in total)
• Functional Keywords: periplasmic peptide binding protein, peptide binding protein
• Biological source: Salmonella typhimurium
• Total number of polymer chains: 2
• Total formula weight: 61212.81

Authors

Davies, T.G.,Tame, J.R.H. (deposition date: 1998-11-16, release date: 1998-11-18, Last modification date: 2024-11-06)

Primary citation

Davies, T.G.,Hubbard, R.E.,Tame, J.R.
Relating structure to thermodynamics: the crystal structures and binding affinity of eight OppA-peptide complexes.
Protein Sci., 8:1432-1444, 1999

PubMed Abstract: The oligopeptide-binding protein OppA provides a useful model system for studying the physical chemistry underlying noncovalent interactions since it binds a variety of readily synthesized ligands. We have studied the binding of eight closely related tripeptides of the type Lysine-X-Lysine, where X is an abnormal amino acid, by isothermal titration calorimetry (ITC) and X-ray crystallography. The tripeptides fall into three series of ligands, which have been designed to examine the effects of small changes to the central side chain. Three ligands have a primary amine as the second side chain, two have a straight alkane chain, and three have ring systems. The results have revealed a definite preference for the binding of hydrophobic residues over the positively charged side chains, the latter binding only weakly due to unfavorable enthalpic effects. Within the series of positively charged groups, a point of lowest affinity has been identified and this is proposed to arise from unfavorable electrostatic interactions in the pocket, including the disruption of a key salt bridge. Marked entropy-enthalpy compensation is found across the series, and some of the difficulties in designing tightly binding ligands have been highlighted.

PubMed: 10422831

Experimental method

X-RAY DIFFRACTION (2 Å)