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- PDB-6e5a: PPARg in complex with compound 4b -

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Basic information

Entry
Database: PDB / ID: 6e5a
TitlePPARg in complex with compound 4b
ComponentsPeroxisome proliferator-activated receptor gamma
KeywordsTRANSCRIPTION / PPAR / nuclear receptor / transcription factor / ligand binding domain
Function / homology
Function and homology information


prostaglandin receptor activity / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / negative regulation of vascular endothelial cell proliferation / negative regulation of extracellular matrix assembly / negative regulation of connective tissue replacement involved in inflammatory response wound healing / positive regulation of cholesterol transport / negative regulation of cellular response to transforming growth factor beta stimulus / : / arachidonate binding ...prostaglandin receptor activity / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / negative regulation of vascular endothelial cell proliferation / negative regulation of extracellular matrix assembly / negative regulation of connective tissue replacement involved in inflammatory response wound healing / positive regulation of cholesterol transport / negative regulation of cellular response to transforming growth factor beta stimulus / : / arachidonate binding / positive regulation of adiponectin secretion / negative regulation of cardiac muscle hypertrophy in response to stress / DNA binding domain binding / lipoprotein transport / positive regulation of vascular associated smooth muscle cell apoptotic process / WW domain binding / STAT family protein binding / positive regulation of fatty acid metabolic process / response to lipid / negative regulation of SMAD protein signal transduction / negative regulation of type II interferon-mediated signaling pathway / LBD domain binding / negative regulation of cholesterol storage / lipid homeostasis / E-box binding / alpha-actinin binding / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / monocyte differentiation / negative regulation of blood vessel endothelial cell migration / white fat cell differentiation / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / cellular response to low-density lipoprotein particle stimulus / negative regulation of BMP signaling pathway / positive regulation of cholesterol efflux / negative regulation of mitochondrial fission / cell fate commitment / negative regulation of osteoblast differentiation / positive regulation of fat cell differentiation / negative regulation of MAPK cascade / BMP signaling pathway / long-chain fatty acid transport / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / retinoic acid receptor signaling pathway / cell maturation / intracellular receptor signaling pathway / positive regulation of adipose tissue development / hormone-mediated signaling pathway / peroxisome proliferator activated receptor signaling pathway / epithelial cell differentiation / regulation of cellular response to insulin stimulus / response to nutrient / negative regulation of miRNA transcription / peptide binding / negative regulation of angiogenesis / transcription coregulator binding / positive regulation of apoptotic signaling pathway / Regulation of PTEN gene transcription / fatty acid metabolic process / placenta development / SUMOylation of intracellular receptors / negative regulation of smooth muscle cell proliferation / negative regulation of transforming growth factor beta receptor signaling pathway / mRNA transcription by RNA polymerase II / PPARA activates gene expression / regulation of circadian rhythm / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / positive regulation of miRNA transcription / regulation of blood pressure / lipid metabolic process / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / RNA polymerase II transcription regulator complex / cellular response to insulin stimulus / nuclear receptor activity / rhythmic process / glucose homeostasis / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / DNA-binding transcription activator activity, RNA polymerase II-specific / double-stranded DNA binding / DNA-binding transcription factor binding / cellular response to hypoxia / sequence-specific DNA binding / nucleic acid binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / receptor complex / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / innate immune response / negative regulation of gene expression / negative regulation of DNA-templated transcription / intracellular membrane-bounded organelle / chromatin binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II
Similarity search - Function
Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Peroxisome proliferator-activated receptor / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type ...Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Peroxisome proliferator-activated receptor / : / Retinoid X Receptor / Retinoid X 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-HV4 / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsBruning, J.B. / Chua, B.S.K. / Frkic, R.L.
CitationJournal: Eur J Med Chem / Year: 2019
Title: Shooting three inflammatory targets with a single bullet: Novel multi-targeting anti-inflammatory glitazones.
Authors: Elzahhar, P.A. / Alaaeddine, R. / Ibrahim, T.M. / Nassra, R. / Ismail, A. / Chua, B.S.K. / Frkic, R.L. / Bruning, J.B. / Wallner, N. / Knape, T. / von Knethen, A. / Labib, H. / El-Yazbi, A.F. / Belal, A.S.F.
History
DepositionJul 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 1.3Dec 18, 2024Group: Structure summary / Category: audit_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peroxisome proliferator-activated receptor gamma
B: Peroxisome proliferator-activated receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1194
Polymers62,5692
Non-polymers5512
Water99155
1
A: Peroxisome proliferator-activated receptor gamma
hetero molecules

B: Peroxisome proliferator-activated receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1194
Polymers62,5692
Non-polymers5512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455x-1/2,y+1/2,z1
Buried area1940 Å2
ΔGint-11 kcal/mol
Surface area23670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.555, 61.163, 118.092
Angle α, β, γ (deg.)90.000, 102.390, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Peroxisome proliferator-activated receptor gamma / PPAR-gamma / Nuclear receptor subfamily 1 group C member 3


Mass: 31284.354 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Cys 285 was modified by BME adduct in protein buffer
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37231
#2: Chemical ChemComp-HV4 / (5Z)-5-({4-[(prop-2-yn-1-yl)oxy]phenyl}methylidene)-2-sulfanylidene-1,3-thiazolidin-4-one


Mass: 275.346 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H9NO2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.62 Å3/Da / Density % sol: 52.97 % / Description: cubic
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 1 M Na Citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 15, 2018 / Details: mirrors - Si ans Rh coatings
RadiationMonochromator: Double Si with sagittaly bent second crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.4→45.53 Å / Num. obs: 25380 / % possible obs: 99.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 61.93 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.034 / Rrim(I) all: 0.087 / Net I/σ(I): 11.6
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.367 / Num. unique obs: 2647 / CC1/2: 0.777 / Rpim(I) all: 0.567 / Rrim(I) all: 1.482 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.34 Å45.53 Å
Translation6.34 Å45.53 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.1data scaling
PHASER2.8.2phasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5U5L

5u5l


Resolution: 2.4→45.53 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.29
RfactorNum. reflection% reflection
Rfree0.2677 1267 5.03 %
Rwork0.2209 --
obs0.2233 25313 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 179.78 Å2 / Biso mean: 90.1499 Å2 / Biso min: 43.94 Å2
Refinement stepCycle: final / Resolution: 2.4→45.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4019 0 36 55 4110
Biso mean--95.77 75.27 -
Num. residues----513
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.49610.39741520.34862622277499
2.4961-2.60970.38891240.333426672791100
2.6097-2.74730.32251540.275226532807100
2.7473-2.91940.37151310.26772681281299
2.9194-3.14480.30091370.257426322769100
3.1448-3.46110.26931410.238326982839100
3.4611-3.96170.27311520.20452650280299
3.9617-4.99030.2311470.19082664281199
4.9903-45.5410.23991340.201827742908100
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)
15.42450.5098-0.10732.9529-1.67052.27320.54690.40120.16960.1430.29540.7866-0.0107-1.902-0.32890.67160.015-0.05180.85440.07730.7116-10.765-4.4944138.6726
22.38222.94070.06486.3403-1.06947.99170.5551-0.2570.37010.4502-0.2234-0.06-1.20750.368-0.40390.56070.02270.10540.5176-0.03270.52681.962310.8653145.2305
39.7542-7.1207-7.03697.79424.88938.7916-0.5417-0.6854-1.4697-1.36570.3733-0.8647-0.37231.0548-0.12761.30590.17440.341.13970.0561.222124.62976.3457146.2446
48.82792.3585-3.91983.14270.52737.7865-0.14090.1116-0.20710.10960.37840.0481-0.5941-1.5911-0.33620.430.21980.00450.94840.10560.5619-24.345418.245126.3084
55.02871.29944.28333.7113.33595.1431-0.95931.00031.7963-2.5659-0.009-1.4138-3.03222.36250.40361.2468-0.5025-0.2190.88480.07990.8931-5.368737.569114.0477
62.78811.0642-1.55342.2318-0.4876.1664-0.1801-0.51440.43120.52310.15990.0323-1.24890.2341-0.03380.87860.2079-0.08420.8363-0.0290.5215-14.490327.4702137.7119
79.98471.08271.60378.3132-2.01399.1024-0.4479-0.5690.36720.35070.0236-1.1007-1.17211.23210.32540.741-0.1579-0.01330.8484-0.0690.5281-3.251628.2401121.5954
83.85880.43891.35793.0117-2.57375.2995-0.2475-0.7894-0.56530.17720.3164-0.19310.4202-0.0771-0.06610.51940.14730.020.72460.07030.5859-15.954411.9086136.8392
97.91234.80261.60333.4861-0.7986.6251-0.4194-0.5371-0.03430.14730.056-1.0395-0.70781.26470.29110.57710.0385-0.0950.79680.010.8165-2.843719.3961136.8511
108.61675.1193-2.6919.35010.22942.85071.4104-0.4202-0.45451.1333-0.9330.4641-0.58790.6886-0.05961.5133-0.00980.01681.4165-0.21541.0055-4.530235.8053140.8421
113.63211.62193.68235.85932.30843.93910.58680.45-1.5403-0.2135-0.329-0.28091.72650.0353-0.43731.0597-0.07280.11010.56320.01510.6505-4.893-14.2141142.7068
121.94031.062.31631.0161-0.55419.42360.6609-1.0115-0.04490.8327-0.2104-0.05920.7850.51980.15880.80090.04580.13371.15290.09260.68294.7234-3.8054163.8139
134.9025-1.3924-5.53872.813-0.94389.11280.2152-3.111-0.44110.7402-0.1969-0.9936-0.14192.7483-0.53530.8705-0.0212-0.00921.72810.15280.698920.04851.9435166.4337
148.60052.77531.71612.75222.37276.15760.5201-0.891-0.16850.3617-0.1729-0.32580.7141.046-0.22730.62080.20410.0990.88650.04830.588313.7804-0.5217149.5113
156.44291.6217-2.04722.1468-0.81288.92610.0362-0.0824-0.2018-0.24620.0942-0.1547-0.5190.2565-0.24340.50810.17660.03670.45940.0430.50426.3302-1.6307138.7316
167.77173.2058-2.26711.8139-1.52728.54330.4104-1.53440.8120.1541-0.17790.3068-1.23480.5136-0.23920.84370.06940.1511.0676-0.08130.62849.13857.9419161.6981
173.4250.0158-0.04430.7318-0.28037.20440.1598-0.1780.3023-0.1542-0.1540.2636-0.5093-0.191-0.180.54880.11990.09020.35950.04560.5786-1.50142.081145.3466
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 403 through 430 )B403 - 430
2X-RAY DIFFRACTION2chain 'B' and (resid 431 through 458 )B431 - 458
3X-RAY DIFFRACTION3chain 'B' and (resid 459 through 476 )B459 - 476
4X-RAY DIFFRACTION4chain 'A' and (resid 205 through 246 )A205 - 246
5X-RAY DIFFRACTION5chain 'A' and (resid 247 through 276 )A247 - 276
6X-RAY DIFFRACTION6chain 'A' and (resid 277 through 333 )A277 - 333
7X-RAY DIFFRACTION7chain 'A' and (resid 334 through 364 )A334 - 364
8X-RAY DIFFRACTION8chain 'A' and (resid 365 through 430 )A365 - 430
9X-RAY DIFFRACTION9chain 'A' and (resid 431 through 459 )A431 - 459
10X-RAY DIFFRACTION10chain 'A' and (resid 460 through 476 )A460 - 476
11X-RAY DIFFRACTION11chain 'B' and (resid 207 through 225 )B207 - 225
12X-RAY DIFFRACTION12chain 'B' and (resid 226 through 251 )B226 - 251
13X-RAY DIFFRACTION13chain 'B' and (resid 252 through 276 )B252 - 276
14X-RAY DIFFRACTION14chain 'B' and (resid 277 through 302 )B277 - 302
15X-RAY DIFFRACTION15chain 'B' and (resid 303 through 333 )B303 - 333
16X-RAY DIFFRACTION16chain 'B' and (resid 334 through 364 )B334 - 364
17X-RAY DIFFRACTION17chain 'B' and (resid 365 through 402 )B365 - 402

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