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PDBsum entry 1b4h
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Peptide binding protein
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PDB id
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1b4h
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Relating structure to thermodynamics: the crystal structures and binding affinity of eight oppa-Peptide complexes.
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Authors
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T.G.Davies,
R.E.Hubbard,
J.R.Tame.
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Ref.
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Protein Sci, 1999,
8,
1432-1444.
[DOI no: ]
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PubMed id
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Abstract
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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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Secondary reference #1
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Title
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The crystal structures of the oligopeptide-Binding protein oppa complexed with tripeptide and tetrapeptide ligands.
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Authors
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J.R.Tame,
E.J.Dodson,
G.Murshudov,
C.F.Higgins,
A.J.Wilkinson.
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Ref.
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Structure, 1995,
3,
1395-1406.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1. Stereo Cα trace of OppA in the closed, ligand bound
form. The tri-lysine ligand is shown in thicker lines. Figure
1. Stereo Cα trace of OppA in the closed, ligand bound form.
The tri-lysine ligand is shown in thicker lines.
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Figure 5.
Figure 5. . Schematic diagram illustrating the interactions
made by the main chain of the tri-lysine ligand with OppA.
Protein residues are labelled. Hydrogen bonding and
electrostatic interactions are indicated by the dotted lines.
R1, R2 and R3 indicate the ligand side chains. Figure 5. .
Schematic diagram illustrating the interactions made by the main
chain of the tri-lysine ligand with OppA. Protein residues are
labelled. Hydrogen bonding and electrostatic interactions are
indicated by the dotted lines. R1, R2 and R3 indicate the ligand
side chains.
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The above figures are
reproduced from the cited reference
with permission from Cell Press
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