4XWK

P-glycoprotein co-crystallized with BDE-100


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.264 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Global marine pollutants inhibit P-glycoprotein: Environmental levels, inhibitory effects, and cocrystal structure.

Nicklisch, S.C.Rees, S.D.McGrath, A.P.Gokirmak, T.Bonito, L.T.Vermeer, L.M.Cregger, C.Loewen, G.Sandin, S.Chang, G.Hamdoun, A.

(2016) Sci Adv 2: e1600001-e1600001

  • DOI: https://doi.org/10.1126/sciadv.1600001
  • Primary Citation of Related Structures:  
    4XWK

  • PubMed Abstract: 

    The world's oceans are a global reservoir of persistent organic pollutants to which humans and other animals are exposed. Although it is well known that these pollutants are potentially hazardous to human and environmental health, their impacts remain incompletely understood. We examined how persistent organic pollutants interact with the drug efflux transporter P-glycoprotein (P-gp), an evolutionarily conserved defense protein that is essential for protection against environmental toxicants. We identified specific congeners of organochlorine pesticides, polychlorinated biphenyls, and polybrominated diphenyl ethers that inhibit mouse and human P-gp, and determined their environmental levels in yellowfin tuna from the Gulf of Mexico. In addition, we solved the cocrystal structure of P-gp bound to one of these inhibitory pollutants, PBDE (polybrominated diphenyl ether)-100, providing the first view of pollutant binding to a drug transporter. The results demonstrate the potential for specific binding and inhibition of mammalian P-gp by ubiquitous congeners of persistent organic pollutants present in fish and other foods, and argue for further consideration of transporter inhibition in the assessment of the risk of exposure to these chemicals.


  • Organizational Affiliation

    Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093-0202, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Multidrug resistance protein 1A1,284Mus musculusMutation(s): 3 
Gene Names: Abcb1aAbcb4Mdr1aMdr3Pgy-3Pgy3
EC: 3.6.3.44
Membrane Entity: Yes 
UniProt
Find proteins for P21447 (Mus musculus)
Explore P21447 
Go to UniProtKB:  P21447
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21447
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4C8
Query on 4C8

Download Ideal Coordinates CCD File 
B [auth A]2,4-dibromophenyl 2,4,6-tribromophenyl ether
C12 H5 Br5 O
NSKIRYMHNFTRLR-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.264 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89α = 90
b = 138.16β = 90
c = 185.15γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United States5R01ES021985-03

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-27
    Type: Initial release
  • Version 1.1: 2016-06-01
    Changes: Database references
  • Version 1.2: 2017-09-06
    Changes: Author supporting evidence, Derived calculations
  • Version 1.3: 2019-12-18
    Changes: Author supporting evidence, Database references
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Refinement description