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- PDB-4xhd: STRUCTURE OF HUMAN PREGNANE X RECEPTOR LIGAND BINDING DOMAIN WITH... -

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Basic information

Entry
Database: PDB / ID: 4xhd
TitleSTRUCTURE OF HUMAN PREGNANE X RECEPTOR LIGAND BINDING DOMAIN WITH COMPOUND-1
ComponentsNuclear receptor subfamily 1 group I member 2
KeywordsTRANSCRIPTION / pregnane X receptor / PXR / ligand binding domain / steroid receptor coactivator-1 / CCR1 / Chemokine Receptor-1 / Adnectin NR / nuclear receptor / AF / activation function / CYP / cytochrome P450 / MDR1 / multi-drug resistance gene-1.
Function / homology
Function and homology information


intermediate filament cytoskeleton / xenobiotic transport / steroid metabolic process / xenobiotic catabolic process / 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 ...intermediate filament cytoskeleton / xenobiotic transport / steroid metabolic process / xenobiotic catabolic process / 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 / regulation of DNA-templated transcription / positive regulation of gene expression / 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
: / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain ...: / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-40U / Nuclear receptor subfamily 1 group I member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsKhan, J.A. / Camac, D.M.
Citation
Journal: J.Mol.Biol. / Year: 2015
Title: Developing Adnectins That Target SRC Co-Activator Binding to PXR: A Structural Approach toward Understanding Promiscuity of PXR.
Authors: Khan, J.A. / Camac, D.M. / Low, S. / Tebben, A.J. / Wensel, D.L. / Wright, M.C. / Su, J. / Jenny, V. / Gupta, R.D. / Ruzanov, M. / Russo, K.A. / Bell, A. / An, Y. / Bryson, J.W. / Gao, M. / ...Authors: Khan, J.A. / Camac, D.M. / Low, S. / Tebben, A.J. / Wensel, D.L. / Wright, M.C. / Su, J. / Jenny, V. / Gupta, R.D. / Ruzanov, M. / Russo, K.A. / Bell, A. / An, Y. / Bryson, J.W. / Gao, M. / Gambhire, P. / Baldwin, E.T. / Gardner, D. / Cavallaro, C.L. / Duncia, J.V. / Hynes, J.
#1: Journal: Bioorg.Med.Chem.Lett. / Year: 2013
Title: The discovery of BMS-457, a potent and selective CCR1 antagonist.
Authors: Gardner, D.S. / Santella, J.B. / Duncia, J.V. / Carter, P.H. / Dhar, T.G. / Wu, H. / Guo, W. / Cavallaro, C. / Van Kirk, K. / Yarde, M. / Briceno, S.W. / Grafstrom, R.R. / Liu, R. / Patel, S. ...Authors: Gardner, D.S. / Santella, J.B. / Duncia, J.V. / Carter, P.H. / Dhar, T.G. / Wu, H. / Guo, W. / Cavallaro, C. / Van Kirk, K. / Yarde, M. / Briceno, S.W. / Grafstrom, R.R. / Liu, R. / Patel, S.R. / Tebben, A.J. / Camac, D. / Khan, J. / Watson, A. / Yang, G. / Rose, A. / Foster, W.R. / Cvijic, M.E. / Davies, P. / Hynes, J.
History
DepositionJan 5, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Sep 30, 2015Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,7373
Polymers36,2241
Non-polymers5132
Water1,22568
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Nuclear receptor subfamily 1 group I member 2
hetero molecules

A: Nuclear receptor subfamily 1 group I member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4746
Polymers72,4482
Non-polymers1,0264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area2480 Å2
ΔGint-13 kcal/mol
Surface area25810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.476, 91.476, 85.564
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Detailschains A

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Components

#1: Protein 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: 36223.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1I2, PXR / Plasmid: pCO7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O75469
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-40U / N-{(2R)-1-[(4S)-4-(4-chlorophenyl)-4-hydroxy-3,3-dimethylpiperidin-1-yl]-3-methyl-1-oxobutan-2-yl}-2-cyclopropylacetamide


Mass: 420.973 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H33ClN2O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O

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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: 2.47 Å3/Da / Density % sol: 50.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.1M imidazole pH 7.8, 8-10%(V/V)isopropanol. Apo crystal was soaked with 5 mM compound 1 and Crystals harvested next day using 32% ethylene glycol as cryoprotectant
PH range: 7.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 14661 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Biso Wilson estimate: 49.61 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 20.9
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.685 / Mean I/σ(I) obs: 3.4 / Rejects: 0 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER-TNTBUSTER 2.11.2refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementResolution: 2.4→45.74 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.9181 / SU R Cruickshank DPI: 0.304 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.321 / SU Rfree Blow DPI: 0.231 / SU Rfree Cruickshank DPI: 0.228
RfactorNum. reflection% reflectionSelection details
Rfree0.2416 737 5.03 %RANDOM
Rwork0.1975 ---
obs0.1997 14643 99.34 %-
Displacement parametersBiso max: 132.98 Å2 / Biso mean: 45.08 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--1.3611 Å20 Å20 Å2
2---1.3611 Å20 Å2
3---2.7222 Å2
Refine analyzeLuzzati coordinate error obs: 0.291 Å
Refinement stepCycle: final / Resolution: 2.4→45.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2177 0 35 68 2280
Biso mean--45.71 44.73 -
Num. residues----268
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d818SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes55HARMONIC2
X-RAY DIFFRACTIONt_gen_planes329HARMONIC5
X-RAY DIFFRACTIONt_it2265HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion283SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2674SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2265HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3056HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion2.68
X-RAY DIFFRACTIONt_other_torsion18.8
LS refinement shellResolution: 2.4→2.59 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2511 169 5.74 %
Rwork0.219 2775 -
all0.2208 2944 -
obs--99.34 %

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