4Y0R

Bovine beta-lactoglobulin complex with pramocaine crystallized from ammonium sulphate (BLG-PRM2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.221 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

beta-Lactoglobulin interactions with local anaesthetic drugs - Crystallographic and calorimetric studies.

Loch, J.I.Bonarek, P.Polit, A.Jabonski, M.Czub, M.Ye, X.Lewinski, K.

(2015) Int J Biol Macromol 80: 87-94

  • DOI: https://doi.org/10.1016/j.ijbiomac.2015.06.013
  • Primary Citation of Related Structures:  
    4Y0P, 4Y0Q, 4Y0R, 4Y0S

  • PubMed Abstract: 

    Interactions between bovine and goat β-lactoglobulin and tetracaine and pramocaine were investigated with isothermal titration calorimetry, X-ray crystallography and molecular modelling. Tetracaine and pramocaine binding to lactoglobulin is an entropy driven endothermic reaction. In this work, we found that determined association constants and thermodynamic parameters indicate that pramocaine has a higher affinity to lactoglobulin than tetracaine. Crystal structures that were determined with resolutions in the range from 1.90 to 2.30 Å revealed in each case the presence of a single drug molecule bound in the β-barrel in a mode similar to that observed for 14- and 16-carbon fatty acids. The position of the ligand in the β-barrel indicates the optimal fit of 6-carbon aromatic rings to the binding pocket and the major role of hydrophobic interactions in ligand binding. Calculations of tetracaine and pramocaine docking to lactoglobulin revealed that molecular modelling overestimated the role of polar protein-drug interactions.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactoglobulin162Bos taurusMutation(s): 0 
UniProt
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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PX9
Query on PX9

Download Ideal Coordinates CCD File 
B [auth A]Pramocaine
C17 H27 N O3
DQKXQSGTHWVTAD-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
PX9 Binding MOAD:  4Y0R Ka: 3000 (M^-1) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.221 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.735α = 90
b = 53.735β = 90
c = 110.738γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
CrysalisProdata collection
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Centre (NCN)Poland--

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-01
    Type: Initial release
  • Version 1.1: 2015-07-08
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description