Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.306 
  • R-Value Observed: 0.210 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history


The Ligand-Binding Site of Bovine Beta-Lactoglobulin: Evidence for a Function?

Kontopidis, G.Holt, C.Sawyer, L.

(2002) J Mol Biol 318: 1043

  • DOI: https://doi.org/10.1016/S0022-2836(02)00017-7
  • Primary Citation of Related Structures:  
    1GX8, 1GX9, 1GXA

  • PubMed Abstract: 

    Ever since the fortuitous observation that beta-lactoglobulin (beta-Lg), the major whey protein in the milk of ruminants, bound retinol, the details of the binding have been controversial. beta-Lg is a lipocalin, like plasma retinol-binding protein, so that ligand association was expected to make use of the central cavity in the protein. However, an early crystallographic analysis and some of the more recent solution studies indicated binding elsewhere. We have now determined the crystal structures of the complexes of the trigonal form of beta-Lg at pH 7.5 with bound retinol (R=21.4% for 7329 reflections between 20 and 2.4 A resolution, R(free)=30.6%) and with bound retinoic acid (R=22.7% for 7813 reflections between 20 and 2.34 A resolution, R(free)=29.8%). Both ligands are found to occupy the central calyx in a manner similar to retinol binding in retinol-binding protein. We find no evidence of binding at the putative external binding site in either of these structural analyses. Further, competition between palmitic acid and retinol reveals only palmitate bound to the protein. An explanation is provided for the lack of ligand binding to the orthorhombic crystal form also obtained at pH 7.5. Finally, the possible function of beta-Lg is discussed in the light of its species distribution and similarity to other lipocalins.

  • Organizational Affiliation

    Structural Biochemistry Group, Institute of Cell and Molecular Biology, The University of Edinburgh, Swann Building, King's Buildings, Mayfield Road, EH9 3JR, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BETA-LACTOGLOBULIN162Bos taurusMutation(s): 0 
Find proteins for P02754 (Bos taurus)
Explore P02754 
Go to UniProtKB:  P02754
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02754
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on RTL

Download Ideal Coordinates CCD File 
C20 H30 O
Binding Affinity Annotations 
IDSourceBinding Affinity
RTL BindingDB:  1GX8 Kd: 36 (nM) from 1 assay(s)
PDBBind:  1GX8 Kd: 430 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.306 
  • R-Value Observed: 0.210 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.579α = 90
b = 53.579β = 90
c = 110.945γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-06-13
    Type: Initial release
  • Version 1.1: 2011-06-02
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-08
    Changes: Data collection, Derived calculations, Experimental preparation, Other
  • Version 1.4: 2019-05-22
    Changes: Data collection, Refinement description
  • Version 1.5: 2023-12-13
    Changes: Data collection, Database references, Refinement description