8CH8 | pdb_00008ch8

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

PDB DOI: https://doi.org/10.2210/pdb8CH8/pdb

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

Deposited: 2023-02-07 Released: 2024-02-21
Deposition Author(s): Carivenc, C., Derosa, Q., Grimaldi, M., Boulahtouf, A., Balaguer, P., Bourguet, W.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.228 (Depositor), 0.234 (DCC)
R-Value Work:
0.206 (Depositor), 0.210 (DCC)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
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Literature

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

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

To be published.

Macromolecule Content

Total Structure Weight: 37.08 kDa
Atom Count: 2,272
Modeled Residue Count: 275
Deposited Residue Count: 320
Unique protein chains: 1

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O75469
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ULC Query on ULC Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	~{O}-(5,6,7,8-tetrahydronaphthalen-2-yl) ~{N}-(6-methoxypyridin-2-yl)-~{N}-methyl-carbamothioate C₁₈ H₂₀ N₂ O₂ S VPHPQNGOVQYUMG-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.228 (Depositor), 0.234 (DCC)
R-Value Work: 0.206 (Depositor), 0.210 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.649	α = 90
b = 91.649	β = 90
c = 85.744	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-02-21

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.