1B2H image
Entry Detail
PDB ID:
1B2H
Title:
Oligo-Peptide Binding Protein Complexed with Lysyl-Ornithyl-Lysine
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
1998-11-16
Release Date:
1998-11-16
Method Details:
Experimental Method:
Resolution:
1.90 Å
R-Value Free:
0.22
R-Value Work:
0.18
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:PERIPLASMIC OLIGOPEPTIDE-BINDING PROTEIN
Chain IDs:A
Chain Length:517
Number of Molecules:1
Biological Source:Salmonella typhimurium
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
ORN B ALA ORNITHINE
Primary Citation
Relating structure to thermodynamics: the crystal structures and binding affinity of eight OppA-peptide complexes.
Protein Sci. 8 1432 1444 (1999)
PMID: 10422831

Abstact

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.

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Primary Citation of related structures