8CF9 | pdb_00008cf9

Crystal structure of the human PXR ligand-binding domain in complex with sclareol

• PDB DOI: https://doi.org/10.2210/pdb8CF9/pdb

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


• Deposited: 2023-02-03 Released: 2024-02-21 
• Deposition Author(s): Carivenc, C., Derosa, Q., Grimaldi, M., Boulahtouf, A., Balaguer, P., Bourguet, W.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.247 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the human PXR ligand-binding domain in complex with sclareol

Carivenc, C., Derosa, Q., Grimaldi, M., Boulahtouf, A., Balaguer, P., Bourguet, W.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 37.15 kDa 
• Atom Count: 2,314 
• Modeled Residue Count: 270 
• Deposited Residue Count: 320 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor subfamily 1 group I member 2	A	320	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UK6 (Subject of Investigation/LOI)	B [auth A]	sclareol C20 H36 O2 XVULBTBTFGYVRC-HHUCQEJWSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.247 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.828	α = 90
b = 91.828	β = 90
c = 85.891	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-21 
Deposition Author(s): Carivenc, C., Derosa, Q., Grimaldi, M., Boulahtouf, A., Balaguer, P., Bourguet, W.

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Funding Organization	Location	Grant Number
Other government	France	ANSES 2018/1/020

Revision History  

• Version 1.0: 2024-02-21
  Type: Initial release