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- PDB-6s41: CRYSTAL STRUCTURE OF PXR IN COMPLEX WITH XPC-7455 -

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Basic information

Entry
Database: PDB / ID: 6s41
TitleCRYSTAL STRUCTURE OF PXR IN COMPLEX WITH XPC-7455
ComponentsNuclear receptor subfamily 1 group I member 2
KeywordsNUCLEAR PROTEIN / PREGNANE X RECEPTOR / NUCLEAR 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-KUB / Nuclear receptor subfamily 1 group I member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsFocken, T. / Maskos, K. / Griessner, A. / Krapp, S.
CitationJournal: J.Med.Chem. / Year: 2019
Title: Identification of CNS-Penetrant Aryl Sulfonamides as Isoform-Selective NaV1.6 Inhibitors with Efficacy in Mouse Models of Epilepsy.
Authors: Focken, T. / Burford, K. / Grimwood, M.E. / Zenova, A. / Andrez, J.C. / Gong, W. / Wilson, M. / Taron, M. / Decker, S. / Lofstrand, V. / Chowdhury, S. / Shuart, N. / Lin, S. / Goodchild, S.J. ...Authors: Focken, T. / Burford, K. / Grimwood, M.E. / Zenova, A. / Andrez, J.C. / Gong, W. / Wilson, M. / Taron, M. / Decker, S. / Lofstrand, V. / Chowdhury, S. / Shuart, N. / Lin, S. / Goodchild, S.J. / Young, C. / Soriano, M. / Tari, P.K. / Waldbrook, M. / Nelkenbrecher, K. / Kwan, R. / Lindgren, A. / de Boer, G. / Lee, S. / Sojo, L. / DeVita, R.J. / Cohen, C.J. / Wesolowski, S.S. / Johnson Jr., J.P. / Dehnhardt, C.M. / Empfield, J.R.
History
DepositionJun 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_gen / pdbx_entity_src_syn / Item: _entity.src_method
Revision 1.2Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.3May 15, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5154
Polymers73,6192
Non-polymers8962
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-16 kcal/mol
Surface area28130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.318, 89.002, 105.815
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 36809.426 Da / Num. of mol.: 2 / Fragment: LIGAND BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1I2, PXR / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O75469
#2: Chemical ChemComp-KUB / 4-[[(1~{S})-1-[2,5-bis(fluoranyl)phenyl]ethyl]amino]-5-chloranyl-2-fluoranyl-~{N}-(1,3-thiazol-4-yl)benzenesulfonamide


Mass: 447.882 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H13ClF3N3O2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.79 Å3/Da / Density % sol: 55.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→68.11 Å / Num. obs: 21795 / % possible obs: 96.9 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 12.16
Reflection shellResolution: 2.7→2.95 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.449 / Num. unique obs: 5020 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→68.11 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.882 / SU B: 29.968 / SU ML: 0.278 / Cross valid method: THROUGHOUT / ESU R: 0.864 / ESU R Free: 0.339 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25901 784 3.6 %RANDOM
Rwork0.21252 ---
obs0.21415 21011 96.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.091 Å2
Baniso -1Baniso -2Baniso -3
1-1.32 Å2-0 Å20 Å2
2---1.22 Å2-0 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.7→68.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4720 0 56 20 4796
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194792
X-RAY DIFFRACTIONr_bond_other_d0.0030.024591
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.9776465
X-RAY DIFFRACTIONr_angle_other_deg1.176310510
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7935571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.06223.575221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.34915855
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.151533
X-RAY DIFFRACTIONr_chiral_restr0.0740.2710
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215332
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021147
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8584.0362305
X-RAY DIFFRACTIONr_mcbond_other2.8254.0312304
X-RAY DIFFRACTIONr_mcangle_it4.7096.7832869
X-RAY DIFFRACTIONr_mcangle_other4.7176.7882870
X-RAY DIFFRACTIONr_scbond_it3.0424.2932487
X-RAY DIFFRACTIONr_scbond_other3.0264.2942487
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7157.133597
X-RAY DIFFRACTIONr_long_range_B_refined7.92535.685159
X-RAY DIFFRACTIONr_long_range_B_other7.92335.6775159
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 59 -
Rwork0.299 1534 -
obs--97.85 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.05531.32541.69625.21112.15026.6614-0.3196-0.32980.6050.3243-0.14030.2085-0.5322-0.480.45980.11930.0594-0.0620.0543-0.05080.114928.31326.21735.373
22.1633-0.10010.74531.2683-0.07113.2461-0.04170.2249-0.2741-0.15330.0142-0.12170.38620.10460.02760.08950.00720.03320.0517-0.01690.06734.49514.99229.703
37.5823-0.39521.25852.55161.79894.31630.12330.16170.0112-0.1633-0.0504-0.0154-0.24090.3653-0.07280.21090.0035-0.02610.19760.03630.228940.67732.26218.294
44.30232.70442.56858.34574.82936.2520.02820.2477-0.4499-0.36290.1609-0.44020.02030.2315-0.18910.04570.0470.0330.14820.03530.0833-5.557-2.985-2.204
53.33041.15280.39472.8680.45522.39970.0016-0.29960.25150.2135-0.0240.1702-0.2733-0.15730.02250.06020.0260.01160.1104-0.00780.0247-12.7432.968.88
64.14192.0231-5.918413.32366.23715.29490.13570.30360.411-0.1193-0.23660.9985-0.4516-0.78440.10090.27140.0517-0.07840.2416-0.03440.2955-13.58217.297-7.468
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A140 - 180
2X-RAY DIFFRACTION2A190 - 435
3X-RAY DIFFRACTION3A682 - 696
4X-RAY DIFFRACTION4B140 - 180
5X-RAY DIFFRACTION5B190 - 435
6X-RAY DIFFRACTION6B682 - 696

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