1B1H

OLIGO-PEPTIDE BINDING PROTEIN/TRIPEPTIDE (LYS HPE LYS) COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Relating structure to thermodynamics: the crystal structures and binding affinity of eight OppA-peptide complexes.

Davies, T.G.Hubbard, R.E.Tame, J.R.

(1999) Protein Sci 8: 1432-1444

  • DOI: 10.1110/ps.8.7.1432
  • Primary Citation of Related Structures:  
    1B0H, 1B1H, 1B2H, 1B3H, 1B4H, 1B5H, 1B6H, 1B7H

  • 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 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.


    Related Citations: 
    • The Crystal Structures of the Oligopeptide-Binding Protein Oppa Complexed with Tripeptide and Tetrapeptide Ligands
      Tame, J.R., Dodson, E.J., Murshudov, G., Higgins, C.F., Wilkinson, A.J.
      (1995) Structure 3: 1395

    Organizational Affiliation

    Department of Chemistry, University of York, Heslington, United Kingdom.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (OLIGO-PEPTIDE BINDING PROTEIN)A517Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
UniProt
Find proteins for P06202 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore P06202 
Go to UniProtKB:  P06202
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06202
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (LYS HPE LYS)B3N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
HPE
Query on HPE
B L-PEPTIDE LINKINGC10 H13 N O2PHE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.722α = 90
b = 75.953β = 90
c = 70.424γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata scaling
REFMACrefinement
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-11-18
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance