3NQ9

Bovine beta-lactoglobulin complex with caprylic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Two modes of fatty acid binding to bovine beta-lactoglobulin-crystallographic and spectroscopic studies

Loch, J.Polit, A.Gorecki, A.Bonarek, P.Kurpiewska, K.Dziedzicka-Wasylewska, M.Lewinski, K.

(2011) J.Mol.Recognit. 24: 341-349

  • DOI: 10.1002/jmr.1084
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Lactoglobulin is a natural protein present in bovine milk and common component of human diet, known for binding with high affinity wide range of hydrophobic compounds, among them fatty acids 12-20 carbon atoms long. Shorter fatty acids were reported ...

    Lactoglobulin is a natural protein present in bovine milk and common component of human diet, known for binding with high affinity wide range of hydrophobic compounds, among them fatty acids 12-20 carbon atoms long. Shorter fatty acids were reported as not binding to β-lactoglobulin. We used X-ray crystallography and fluorescence spectroscopy to show that lactoglobulin binds also 8- and 10-carbon caprylic and capric acids, however with lower affinity. The determined apparent association constant for lactoglobulin complex with caprylic acid is 10.8 ± 1.7 × 10(3) M(-1), while for capric acid is 6.0 ± 0.5 × 10(3) M(-1). In crystal structures determined with resolution 1.9 Å the caprylic acid is bound in upper part of central calyx near polar residues located at CD loop, while the capric acid is buried deeper in the calyx bottom and does not interact with polar residues at CD loop. In both structures, water molecule hydrogen-bonded to carboxyl group of fatty acid is observed. Different location of ligands in the binding site indicates that competition between polar and hydrophobic interactions is an important factor determining position of the ligand in β-barrel.


    Organizational Affiliation

    Faculty of Chemistry, Department of Crystal Physics and Crystal Chemistry, Jagiellonian University, Ingardena 3, 30-060 Kraków, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactoglobulin
A
162Bos taurusMutation(s): 0 
Gene Names: LGB
Find proteins for P02754 (Bos taurus)
Go to UniProtKB:  P02754
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
OCA
Query on OCA

Download SDF File 
Download CCD File 
A
OCTANOIC ACID (CAPRYLIC ACID)
C8 H16 O2
WWZKQHOCKIZLMA-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
OCAKd: 92600 nM BINDINGMOAD
OCAKd: 92600 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.233 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 53.470α = 90.00
b = 53.470β = 90.00
c = 112.060γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
CrysalisProdata collection
CrysalisProdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-06-29 
  • Released Date: 2010-07-14 
  • Deposition Author(s): Loch, J., Lewinski, K.

Revision History 

  • Version 1.0: 2010-07-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance