Structure of oligo-peptide binding protein complexed with LYS-CYS-LYS

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.198 

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Crystallographic and calorimetric analysis of peptide binding to OppA protein.

Sleigh, S.H.Seavers, P.R.Wilkinson, A.J.Ladbury, J.E.Tame, J.R.

(1999) J Mol Biol 291: 393-415

  • DOI: https://doi.org/10.1006/jmbi.1999.2929
  • Primary Citation of Related Structures:  
    1B05, 1B32, 1B3F, 1B3G, 1B3L, 1B40, 1B46, 1B4Z, 1B51, 1B52, 1B58, 1B5I, 1B5J, 1B9J, 1QKA, 1QKB

  • PubMed Abstract: 

    Isothermal titration calorimetry has been used to study the binding of 20 different peptides to the peptide binding protein OppA, and the crystal structures of the ligand complexes have been refined. This periplasmic binding protein, part of the oligopeptide permease system of Gram negative bacteria, has evolved to bind and enclose small peptides of widely varying sequences. The peptides used in this study have the sequence Lys-X-Lys, where X is any of the 20 commonly occurring amino acids. The various side-chains found at position 2 on the ligand fit into a hydrated pocket. The majority of side-chains are restrained to particular conformations within the pocket. Water molecules act as flexible adapters, matching the hydrogen-bonding requirements of the protein and ligand and shielding charges on the buried ligand. This use of water by OppA to broaden the repertoire of its binding site is not unique, but contrasts sharply with other proteins which use water to help bind ligands highly selectively. Predicting the thermodynamics of binding from the structure of the complexes is highly complicated by the influence of water on the system.

  • Organizational Affiliation

    Structural Biology Centre Department of Chemistry, University of York, York, YO10 5DD, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PERIPLASMIC OLIGOPEPTIDE-BINDING PROTEIN517Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
Gene Names: OPPA
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
Sequence Annotations
  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PEPTIDE LYS-CYS-LYS3N/AMutation(s): 0 
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.55α = 90
b = 76.12β = 90
c = 70.5γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata scaling
CCP4model building
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-11-25
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-09
    Changes: Data collection, Database references, Derived calculations, Refinement description