1B6H

OLIGO-PEPTIDE BINDING PROTEIN COMPLEXED WITH LYSYL-NORVALYL-LYSINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.180 

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, 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 ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PERIPLASMIC OLIGO-PEPTIDE BINDING PROTEIN
A
517Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)Gene Names: oppA
Find proteins for P06202 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  P06202
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
LYS-NVA-LYS PEPTIDE
B
3N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
U1
Query on U1

Download SDF File 
Download CCD File 
A
URANIUM ATOM
U
JFALSRSLKYAFGM-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
NVA
Query on NVA
B
L-PEPTIDE LINKINGC5 H11 N O2VAL
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 109.680α = 90.00
b = 75.770β = 90.00
c = 70.250γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata scaling
CCP4data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-11-18
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance