4Y0S | pdb_00004y0s

Goat beta-lactoglobulin complex with pramocaine (GLG-PRM)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.265 (Depositor), 0.269 (DCC) 
  • R-Value Work: 
    0.213 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 
    0.219 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 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 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.

Macromolecule Content 

  • Total Structure Weight: 18.7 kDa 
  • Atom Count: 1,383 
  • Modeled Residue Count: 157 
  • Deposited Residue Count: 162 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-lactoglobulin162Capra hircusMutation(s): 0 
UniProt
Find proteins for P02756 (Capra hircus)
Explore P02756 
Go to UniProtKB:  P02756
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02756
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.265 (Depositor), 0.269 (DCC) 
  • R-Value Work:  0.213 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 0.219 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.113α = 90
b = 53.113β = 90
c = 111.148γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
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
  • Version 1.3: 2024-10-23
    Changes: Structure summary