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- PDB-7n2a: human PXR LBD bound to compound 2 -

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Basic information

Entry
Database: PDB / ID: 7n2a
Titlehuman PXR LBD bound to compound 2
ComponentsIsoform 1C of Nuclear receptor subfamily 1 group I member 2
KeywordsGENE REGULATION / nuclear receptor / helical sandwich / xenobiotics
Function / homology
Function and homology information


cellular response to molecule of bacterial origin / intestinal epithelial structure maintenance / intermediate filament cytoskeleton / xenobiotic transport / steroid metabolic process / xenobiotic catabolic process / intracellular receptor signaling pathway / xenobiotic metabolic process / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding ...cellular response to molecule of bacterial origin / intestinal epithelial structure maintenance / intermediate filament cytoskeleton / xenobiotic transport / steroid metabolic process / xenobiotic catabolic process / intracellular receptor signaling pathway / xenobiotic metabolic process / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / positive regulation of gene expression / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
: / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor ...: / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type
Similarity search - Domain/homology
Chem-07F / Nuclear receptor subfamily 1 group I member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.26 Å
AuthorsWilliams, S.P. / Wisely, G.B. / Ramanjulu, J.M.
CitationJournal: Acs Med.Chem.Lett. / Year: 2021
Title: Overcoming the Pregnane X Receptor Liability: Rational Design to Eliminate PXR-Mediated CYP Induction.
Authors: Ramanjulu, J.M. / Williams, S.P. / Lakdawala, A.S. / DeMartino, M.P. / Lan, Y. / Marquis, R.W.
History
DepositionMay 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 1C of Nuclear receptor subfamily 1 group I member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6022
Polymers34,1881
Non-polymers4141
Water84747
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.512, 91.512, 85.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Isoform 1C of Nuclear receptor subfamily 1 group I member 2 / Orphan nuclear receptor PAR1 / Orphan nuclear receptor PXR / Pregnane X receptor / Steroid and ...Orphan nuclear receptor PAR1 / Orphan nuclear receptor PXR / Pregnane X receptor / Steroid and xenobiotic receptor / SXR


Mass: 34187.562 Da / Num. of mol.: 1 / Fragment: ligand binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1I2, PXR / Plasmid: pRSETa / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O75469
#2: Chemical ChemComp-07F / 5-benzyl-2-(3-fluoro-2-hydroxyphenyl)-6-methyl-3-(2-phenylethyl)pyrimidin-4(3H)-one


Mass: 414.471 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H23FN2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.77 % / Description: Multi-faceted diamonds
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 50mM Imidazole pH7.2, 12% 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9787 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 21, 2008 / Details: Toroidal Mirror
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.26→50 Å / Num. obs: 17369 / % possible obs: 99.1 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.072 / Χ2: 1.246 / Net I/σ(I): 10 / Num. measured all: 164067
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.26-2.349.70.53317080.7641100
2.34-2.439.60.40817260.7691100
2.43-2.559.70.34317180.805199.9
2.55-2.689.70.22417020.862199.9
2.68-2.859.60.16317300.898199.9
2.85-3.079.60.1117251.0041100
3.07-3.389.50.07317531.1341100
3.38-3.869.30.06317591.972199.8
3.86-4.878.90.05517502.645198.4
4.87-5090.0417981.745193.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å35.54 Å
Translation2.5 Å35.54 Å

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASER1.3.3phasing
REFMAC5.5.0053refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 1ILH

1ilh


Resolution: 2.26→35.53 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.2556 / WRfactor Rwork: 0.2353 / FOM work R set: 0.8207 / SU B: 6.087 / SU ML: 0.153 / SU R Cruickshank DPI: 0.31 / SU Rfree: 0.228 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.292 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1222 7.1 %RANDOM
Rwork0.2301 ---
obs0.2319 16098 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.75 Å2 / Biso mean: 38.31 Å2 / Biso min: 28.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å20 Å2
2--0.57 Å20 Å2
3----1.15 Å2
Refinement stepCycle: final / Resolution: 2.26→35.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2110 0 31 47 2188
Biso mean--83.74 51.2 -
Num. residues----273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222198
X-RAY DIFFRACTIONr_bond_other_d0.0010.021471
X-RAY DIFFRACTIONr_angle_refined_deg0.9161.9822977
X-RAY DIFFRACTIONr_angle_other_deg0.7833579
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2055273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.67123.62691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.54215361
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2961512
X-RAY DIFFRACTIONr_chiral_restr0.0430.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212479
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02476
LS refinement shellResolution: 2.261→2.32 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 88 -
Rwork0.266 1184 -
all-1272 -
obs--100 %

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