1SKX

Structural Disorder in the Complex of Human PXR and the Macrolide Antibiotic Rifampicin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.287 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural disorder in the complex of human pregnane x receptor and the macrolide antibiotic rifampicin

Chrencik, J.E.Orans, J.O.Moore, L.B.Xue, Y.Peng, L.Collins, J.L.Wisely, G.B.Lambert, M.H.Kliewer, S.A.Redinbo, M.R.

(2005) Mol Endocrinol 19: 1125-1134

  • DOI: https://doi.org/10.1210/me.2004-0346
  • Primary Citation of Related Structures:  
    1SKX

  • PubMed Abstract: 

    The human nuclear xenobiotic receptor, pregnane X receptor (PXR), detects a variety of structurally distinct endogenous and xenobiotic compounds and controls expression of genes central to drug and cholesterol metabolism. The macrolide antibiotic rifampicin, a front-line treatment for tuberculosis, is an established PXR agonist and, at 823 Da, is one of the largest known ligands for the receptor. We present the 2.8 A crystal structure of the ligand-binding domain of human PXR in complex with rifampicin. We also use structural and mutagenesis data to examine the origins of the directed promiscuity exhibited by the PXRs across species. Three structurally flexible loops adjacent to the ligand-binding pocket of PXR are disordered in this crystal structure, including the 200-210 region that is part of a sequence insert novel to the promiscuous PXRs relative to other members of the nuclear receptor superfamily. The 4-methyl-1-piperazinyl ring of rifampicin, which would lie adjacent to the disordered protein regions, is also disordered and not observed in the structure. Taken together, our results indicate that one wall of the PXR ligand-binding cavity can remain flexible even when the receptor is in complex with an activating ligand. These observations highlight the key role that structural flexibility plays in PXR's promiscuous response to xenobiotics.


  • Organizational Affiliation

    Department of Chemistry, Campus Box 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Orphan nuclear receptor PXR313Homo sapiensMutation(s): 0 
Gene Names: NR1I2PXR
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RFP
Query on RFP

Download Ideal Coordinates CCD File 
B [auth A]RIFAMPICIN
C43 H58 N4 O12
JQXXHWHPUNPDRT-WLSIYKJHSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
RFP BindingDB:  1SKX EC50: min: 190, max: 5600 (nM) from 11 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.287 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.537α = 90
b = 91.537β = 90
c = 85.504γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
TRUNCATEdata reduction
AMoREphasing
CNSrefinement
HKL-2000data reduction
CCP4data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-03-08
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description