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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.284 (Depositor), 0.277 (DCC)
R-Value Work:
0.242 (Depositor), 0.237 (DCC)
R-Value Observed:
0.242 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 2QNV

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of the Pregnane X Receptor bound to Colupulone

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

To be published.

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

Find similar proteins by:

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
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
CDZ Query on CDZ 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]	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		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.284 (Depositor), 0.277 (DCC)
R-Value Work: 0.242 (Depositor), 0.237 (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

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-07-29

Deposition Author(s):

Revision History (Full details and data files)

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

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.