1ILG | pdb_00001ilg

Crystal Structure of Apo Human Pregnane X Receptor Ligand Binding Domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 
    0.279 (Depositor), 0.278 (DCC) 
  • R-Value Work: 
    0.215 (Depositor), 0.215 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

The human nuclear xenobiotic receptor PXR: structural determinants of directed promiscuity.

Watkins, R.E.Wisely, G.B.Moore, L.B.Collins, J.L.Lambert, M.H.Williams, S.P.Willson, T.M.Kliewer, S.A.Redinbo, M.R.

(2001) Science 292: 2329-2333

  • DOI: https://doi.org/10.1126/science.1060762
  • Primary Citation Related Structures: 
    1ILG, 1ILH

  • PubMed Abstract: 

    The human nuclear pregnane X receptor (hPXR) activates cytochrome P450-3A expression in response to a wide variety of xenobiotics and plays a critical role in mediating dangerous drug-drug interactions. We present the crystal structures of the ligand-binding domain of hPXR both alone and in complex with the cholesterol-lowering drug SR12813 at resolutions of 2.5 and 2.75 angstroms, respectively. The hydrophobic ligand-binding cavity of hPXR contains a small number of polar residues, permitting SR12813 to bind in three distinct orientations. The position and nature of these polar residues were found to be critical for establishing the precise pharmacologic activation profile of PXR. Our findings provide important insights into how hPXR detects xenobiotics and may prove useful in predicting and avoiding drug-drug interactions.


  • Organizational Affiliation
    • Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina (UNC) at Chapel Hill, Chapel Hill, NC 27599, USA.

Macromolecule Content 

  • Total Structure Weight: 36.28 kDa 
  • Atom Count: 2,391 
  • Modeled Residue Count: 270 
  • Deposited Residue Count: 316 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ORPHAN NUCLEAR RECEPTOR PXR316Homo sapiensMutation(s): 0 
Gene Names: PXR
UniProt & NIH Common Fund Data Resources
Find proteins for O75469 (Homo sapiens)
Explore O75469 
Go to UniProtKB:  O75469
PHAROS:  O75469
GTEx:  ENSG00000144852 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75469
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free:  0.279 (Depositor), 0.278 (DCC) 
  • R-Value Work:  0.215 (Depositor), 0.215 (DCC) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.59α = 90
b = 91.59β = 90
c = 84.98γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
MAR345data collection
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-06-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2023-08-16
    Changes: Data collection, Database references, Refinement description