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- PDB-5q1d: Ligand binding to FARNESOID-X-RECEPTOR -

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Basic information

Entry
Database: PDB / ID: 5q1d
TitleLigand binding to FARNESOID-X-RECEPTOR
Components
  • Bile acid receptor
  • COACTIVATOR PEPTIDE SRC-1 HD3
KeywordsTRANSCRIPTION / D3R / FXR / Docking
Function / homology
Function and homology information


regulation of urea metabolic process / intracellular bile acid receptor signaling pathway / chenodeoxycholic acid binding / positive regulation of phosphatidic acid biosynthetic process / positive regulation of glutamate metabolic process / positive regulation of ammonia assimilation cycle / bile acid receptor activity / regulation of low-density lipoprotein particle clearance / intracellular triglyceride homeostasis / cellular response to bile acid ...regulation of urea metabolic process / intracellular bile acid receptor signaling pathway / chenodeoxycholic acid binding / positive regulation of phosphatidic acid biosynthetic process / positive regulation of glutamate metabolic process / positive regulation of ammonia assimilation cycle / bile acid receptor activity / regulation of low-density lipoprotein particle clearance / intracellular triglyceride homeostasis / cellular response to bile acid / negative regulation of very-low-density lipoprotein particle remodeling / negative regulation of interleukin-1 production / regulation of bile acid biosynthetic process / regulation of insulin secretion involved in cellular response to glucose stimulus / cellular response to organonitrogen compound / toll-like receptor 9 signaling pathway / negative regulation of monocyte chemotactic protein-1 production / intracellular receptor signaling pathway / bile acid metabolic process / nitrogen catabolite activation of transcription from RNA polymerase II promoter / labyrinthine layer morphogenesis / regulation of thyroid hormone mediated signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / cell-cell junction assembly / bile acid binding / bile acid signaling pathway / negative regulation of interleukin-2 production / cellular response to fatty acid / regulation of cholesterol metabolic process / hypothalamus development / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / positive regulation of interleukin-17 production / intracellular glucose homeostasis / positive regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of interleukin-6 production / negative regulation of type II interferon production / estrous cycle / negative regulation of tumor necrosis factor production / cellular response to Thyroglobulin triiodothyronine / Synthesis of bile acids and bile salts / negative regulation of tumor necrosis factor-mediated signaling pathway / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / fatty acid homeostasis / nuclear retinoid X receptor binding / response to retinoic acid / negative regulation of canonical NF-kappaB signal transduction / positive regulation of insulin receptor signaling pathway / histone acetyltransferase activity / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / Notch signaling pathway / histone acetyltransferase / cellular response to hormone stimulus / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / lactation / positive regulation of neuron differentiation / Regulation of lipid metabolism by PPARalpha / cerebellum development / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / response to progesterone / cholesterol homeostasis / transcription coregulator binding / nuclear estrogen receptor binding / nuclear receptor binding / hippocampus development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Heme signaling / euchromatin / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / cerebral cortex development / negative regulation of inflammatory response / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / male gonad development / nuclear receptor activity / Circadian Clock / response to estradiol / HATs acetylate histones / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / cellular response to lipopolysaccharide / transcription regulator complex / sequence-specific DNA binding / transcription by RNA polymerase II / cell differentiation
Similarity search - Function
Bile acid receptor, ligand binding domain / Thyroid hormone receptor / Nuclear receptor coactivator 1 / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain ...Bile acid receptor, ligand binding domain / Thyroid hormone receptor / Nuclear receptor coactivator 1 / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / PAS domain / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Nuclear receptor coactivator, interlocking / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 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-9ND / Nuclear receptor coactivator / Nuclear receptor coactivator 1 / Bile acid receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.89 Å
Model detailsStructures re-refined for D3R docking challenge
AuthorsRudolph, M.G. / Benz, J. / Burger, D. / Thoma, R. / Ruf, A. / Joseph, C. / Kuhn, B. / Shao, C. / Yang, H. / Burley, S.K.
CitationJournal: J. Comput. Aided Mol. Des. / Year: 2018
Title: D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.
Authors: Gaieb, Z. / Liu, S. / Gathiaka, S. / Chiu, M. / Yang, H. / Shao, C. / Feher, V.A. / Walters, W.P. / Kuhn, B. / Rudolph, M.G. / Burley, S.K. / Gilson, M.K. / Amaro, R.E.
History
DepositionMay 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Structure summary / Category: audit_author / citation_author
Revision 1.2Dec 20, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 31, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.4Feb 21, 2018Group: Structure summary / Category: pdbx_deposit_group / Item: _pdbx_deposit_group.group_type
Revision 1.5Feb 10, 2021Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.identifier_ORCID / _citation.country / _citation_author.identifier_ORCID
Revision 1.6Nov 17, 2021Group: Database references / Structure summary / Category: database_2 / pdbx_deposit_group
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_deposit_group.group_description

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bile acid receptor
B: COACTIVATOR PEPTIDE SRC-1 HD3
C: Bile acid receptor
D: COACTIVATOR PEPTIDE SRC-1 HD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7406
Polymers57,7804
Non-polymers9602
Water6,972387
1
A: Bile acid receptor
B: COACTIVATOR PEPTIDE SRC-1 HD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3703
Polymers28,8902
Non-polymers4801
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-7 kcal/mol
Surface area12150 Å2
MethodPISA
2
C: Bile acid receptor
D: COACTIVATOR PEPTIDE SRC-1 HD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3703
Polymers28,8902
Non-polymers4801
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-6 kcal/mol
Surface area12070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.440, 84.530, 190.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-782-

HOH

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Components

#1: Protein Bile acid receptor / Farnesoid X-activated receptor / Farnesol receptor HRR-1 / Nuclear receptor subfamily 1 group H ...Farnesoid X-activated receptor / Farnesol receptor HRR-1 / Nuclear receptor subfamily 1 group H member 4 / Retinoid X receptor-interacting protein 14 / RXR-interacting protein 14


Mass: 27100.191 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1H4, BAR, FXR, HRR1, RIP14 / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / References: UniProt: Q96RI1
#2: Protein/peptide COACTIVATOR PEPTIDE SRC-1 HD3


Mass: 1790.026 Da / Num. of mol.: 2 / Fragment: UNP residues 744-757 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: A8K1V4, UniProt: Q15788*PLUS
#3: Chemical ChemComp-9ND / (2S)-2-[2-(4-chlorophenyl)-5,6-difluoro-1H-benzimidazol-1-yl]-2-cyclohexyl-N-phenylacetamide


Mass: 479.949 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H24ClF2N3O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 387 / 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: 2.57 Å3/Da / Density % sol: 52.2 %
Crystal growTemperature: 298 K / Method: evaporation, hanging drop / pH: 6.5
Details: 0.2 M Na Chloride, 0.1 M Bis-Tris pH 6.5, 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 13, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→47.7 Å / Num. all: 46821 / Num. obs: 46610 / % possible obs: 99.5 % / Redundancy: 6.43 % / Rmerge(I) obs: 0.0904 / Net I/σ(I): 11.06
Reflection shellResolution: 1.9→2 Å / Redundancy: 6.21 % / Rmerge(I) obs: 0.8429 / Num. possible: 6608 / Num. unique obs: 6441 / Net I/σ(I) obs: 1.48 / % possible all: 97.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTER2.10.3refinement
HKL-2000data scaling
PDB_EXTRACT3.23data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→27.67 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.928 / SU R Cruickshank DPI: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.159 / SU Rfree Blow DPI: 0.145 / SU Rfree Cruickshank DPI: 0.142
RfactorNum. reflection% reflectionSelection details
Rfree0.244 2360 5.03 %RANDOM
Rwork0.206 ---
obs0.208 46940 99.4 %-
Displacement parametersBiso max: 147.71 Å2 / Biso mean: 47.34 Å2 / Biso min: 6.3 Å2
Baniso -1Baniso -2Baniso -3
1-5.0964 Å20 Å20 Å2
2---2.1442 Å20 Å2
3----2.9522 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: final / Resolution: 1.89→27.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3956 0 68 387 4411
Biso mean--31.94 53.52 -
Num. residues----482
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1495SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes118HARMONIC2
X-RAY DIFFRACTIONt_gen_planes577HARMONIC5
X-RAY DIFFRACTIONt_it4141HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion531SEMIHARMONIC5
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_contact5045SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4141HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg5601HARMONIC20.94
X-RAY DIFFRACTIONt_omega_torsion2.2
X-RAY DIFFRACTIONt_other_torsion18.23
LS refinement shellResolution: 1.89→1.94 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4982 171 5.13 %
Rwork0.4939 3165 -
all0.4941 3336 -
obs--96.44 %
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)
11.51480.10560.86722.12450.62565.0301-0.0878-0.05210.0763-0.0936-0.00670.0621-0.3221-0.03630.09460.0305-0.03670.0407-0.10650.0168-0.111611.772720.6859-6.4525
20.8274-0.6912-0.53520.99730.6940.58350.00980.0032-0.006-0.03330.0308-0.05780.04990.0565-0.04050.1659-0.0228-0.0319-0.08190.027-0.011720.71021.6522-5.9175
32.4423-0.5462-0.35152.05240.26992.2396-0.0282-0.1563-0.064-0.0015-0.0520.0729-0.00360.05830.08020.010.07190.01990.02470.0286-0.150719.900553.267334.7485
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A247 - 476
2X-RAY DIFFRACTION2{ B|* }B744 - 754
3X-RAY DIFFRACTION3{ C|* }C247 - 476

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