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- PDB-4s0t: STRUCTURE OF HUMAN PREGNANE X RECEPTOR LIGAND BINDING DOMAIN BOUN... -

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Basic information

Entry
Database: PDB / ID: 4s0t
TitleSTRUCTURE OF HUMAN PREGNANE X RECEPTOR LIGAND BINDING DOMAIN BOUND WITH ADNECTIN-1 AND COMPOUND-1
Components
  • Adnectin-1
  • Nuclear receptor subfamily 1 group I member 2
KeywordsTRANSCRIPTION / NUCLEAR RECEPTOR / MULTIPLE BINDING MODES / XENOBIOTIC / PROMISCUOUS / NUCLEAR HORMONE RECEPTOR
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 / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / 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 / MOLECULAR REPLACEMENT / Resolution: 3.14 Å
AuthorsKhan, J.A. / Camac, D.M.
CitationJournal: 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.
History
DepositionJan 5, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Nov 29, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_id
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
B: Nuclear receptor subfamily 1 group I member 2
D: Adnectin-1
E: Adnectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,7556
Polymers98,9134
Non-polymers8422
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-35 kcal/mol
Surface area34400 Å2
MethodPISA
2
A: Nuclear receptor subfamily 1 group I member 2
D: Adnectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8773
Polymers49,4562
Non-polymers4211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-13 kcal/mol
Surface area17850 Å2
MethodPISA
3
B: Nuclear receptor subfamily 1 group I member 2
E: Adnectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8773
Polymers49,4562
Non-polymers4211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-13 kcal/mol
Surface area17920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.871, 119.871, 84.186
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

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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.: 2
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: Protein Adnectin-1


Mass: 13232.593 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-9D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
#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.: 2 / Source method: obtained synthetically / Formula: C23H33ClN2O3

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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: 3.06 Å3/Da / Density % sol: 59.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Tris pH 7.5, 10%(V/V)isopropanol, 3.5% (V/V) MPD. Apo crystal was soaked with 5 mM compound 1 and Crystals harvested next day using Paratone-N as cryoprotectant, VAPOR DIFFUSION, ...Details: 0.1M Tris pH 7.5, 10%(V/V)isopropanol, 3.5% (V/V) MPD. Apo crystal was soaked with 5 mM compound 1 and Crystals harvested next day using Paratone-N as cryoprotectant, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 23, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 3.14→42.38 Å / Num. obs: 20764 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 105.84 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 13.3
Reflection shellResolution: 3.14→3.31 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 3.9 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
BUSTER-TNTBUSTER 2.11.6refinement
PDB_EXTRACT3.15data extraction
BUSTER2.11.6refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.14→42.38 Å / Cor.coef. Fo:Fc: 0.9241 / Cor.coef. Fo:Fc free: 0.9047 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2475 1068 5.15 %RANDOM
Rwork0.2136 ---
obs0.2153 20742 98.63 %-
Displacement parametersBiso mean: 92.99 Å2
Baniso -1Baniso -2Baniso -3
1--11.877 Å20 Å20 Å2
2---11.877 Å20 Å2
3---23.754 Å2
Refine analyzeLuzzati coordinate error obs: 0.632 Å
Refinement stepCycle: LAST / Resolution: 3.14→42.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5727 0 58 0 5785
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015942HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.278105HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1941SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes124HARMONIC2
X-RAY DIFFRACTIONt_gen_planes866HARMONIC5
X-RAY DIFFRACTIONt_it5942HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3
X-RAY DIFFRACTIONt_other_torsion22.51
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion792SEMIHARMONIC5
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_contact6900SEMIHARMONIC4
LS refinement shellResolution: 3.14→3.31 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.273 167 5.61 %
Rwork0.2334 2811 -
all0.2356 2978 -
obs--98.63 %

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