Lactococcal OppA complexed with SLSQLSSQS

Experimental Data Snapshot

  • Resolution: 2.90 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 

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This is version 1.3 of the entry. See complete history


Importance of a Hydrophobic Pocket for Peptide Binding in Lactococcal OppA.

Berntsson, R.P.Thunnissen, A.M.Poolman, B.Slotboom, D.J.

(2011) J Bacteriol 193: 4254-4256

  • DOI: https://doi.org/10.1128/JB.00447-11
  • Primary Citation of Related Structures:  
    3RYA, 3RYB

  • PubMed Abstract: 

    Lactococcal oligopeptide-binding protein A (OppA) binds peptides with widely varied lengths and sequences. We previously hypothesized that a hydrophobic pocket in OppA preferentially binds a hydrophobic peptide side chain and thus determines its binding register. Two crystal structures of OppA with different nonapeptides now indeed show binding in different registers.

  • Organizational Affiliation

    Biochemistry Department, Groningen Biomolecular Sciences and Biotechnology Center, NPC & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Oligopeptide-binding protein oppA590Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
Gene Names: oppAllmg_0701
Find proteins for A2RJ53 (Lactococcus lactis subsp. cremoris (strain MG1363))
Explore A2RJ53 
Go to UniProtKB:  A2RJ53
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA2RJ53
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Oligopeptide9N/AMutation(s): 0 
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.90 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.628α = 90
b = 99.555β = 90
c = 123.91γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
MAR345dtbdata collection
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-08-10
    Changes: Database references
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Refinement description