1GX8

BOVINE BETA-LACTOGLOBULIN COMPLEXED WITH RETINOL, TRIGONAL LATTICE Z


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.306 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

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

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BETA-LACTOGLOBULIN A162Bos taurusMutation(s): 0 
Gene Names: LGB
Find proteins for P02754 (Bos taurus)
Explore P02754 
Go to UniProtKB:  P02754
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RTL
Query on RTL

Download Ideal Coordinates CCD File 
A
RETINOL
C20 H30 O
FPIPGXGPPPQFEQ-OVSJKPMPSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RTLKd:  36   nM  BindingDB
RTLKd :  430   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing

Structure Validation

View Full Validation Report



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