2QNV | pdb_00002qnv

Crystal Structure of the Pregnane X Receptor bound to Colupulone

• PDB DOI: https://doi.org/10.2210/pdb2QNV/pdb

• Classification: NUCLEAR PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-07-19 Released: 2008-07-29 
• Deposition Author(s): Teotico, D.G., Bischof, J., Redinbo, M.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.284 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.242 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.242 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the Pregnane X Receptor bound to Colupulone

Teotico, D.G., Bischof, J., Redinbo, M.R.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 36.68 kDa 
• Atom Count: 2,043 
• Modeled Residue Count: 249 
• Deposited Residue Count: 316 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orphan nuclear receptor PXR	A	316	Homo sapiens	Mutation(s): 0  Gene Names: NR1I2, PXR
UniProt & NIH Common Fund Data Resources
Find proteins for O75469 (Homo sapiens) Explore O75469  Go to UniProtKB:  O75469
PHAROS:  O75469 GTEx:  ENSG00000144852

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CDZ	B [auth A]	3,5-dihydroxy-4,6,6-tris(3-methylbut-2-en-1-yl)-2-(2-methylpropanoyl)cyclohexa-2,4-dien-1-one C25 H36 O4 UNCDMWKTFLUPHZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.284 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.242 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.242 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.865	α = 90
b = 90.865	β = 90
c = 85.41	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-29 
Deposition Author(s): Teotico, D.G., Bischof, J., Redinbo, M.R.

Revision History  

• Version 1.0: 2008-07-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-04-15
  Changes: Data collection, Database references, Source and taxonomy, Structure summary
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description