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- PDB-7lot: Human PPAR Gamma LBD in Complex with Tetrazole Compound N-{3-[(4-... -

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Basic information

Entry
Database: PDB / ID: 7lot
TitleHuman PPAR Gamma LBD in Complex with Tetrazole Compound N-{3-[(4-methylbenzyl)oxy]benzyl}-2H-tetrazol-5-amine.
ComponentsPeroxisome proliferator-activated receptor gamma
KeywordsGENE REGULATION / PPAR gamma / Complex / Tetrazole
Function / homology
Function and homology information


prostaglandin receptor activity / regulation of cholesterol transporter activity / negative regulation of connective tissue replacement involved in inflammatory response wound healing / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / negative regulation of extracellular matrix assembly / negative regulation of vascular endothelial cell proliferation / negative regulation of cellular response to transforming growth factor beta stimulus / negative regulation of cardiac muscle hypertrophy in response to stress / arachidonic acid binding ...prostaglandin receptor activity / regulation of cholesterol transporter activity / negative regulation of connective tissue replacement involved in inflammatory response wound healing / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / negative regulation of extracellular matrix assembly / negative regulation of vascular endothelial cell proliferation / negative regulation of cellular response to transforming growth factor beta stimulus / negative regulation of cardiac muscle hypertrophy in response to stress / arachidonic acid binding / positive regulation of low-density lipoprotein receptor activity / positive regulation of adiponectin secretion / lipoprotein transport / negative regulation of sequestering of triglyceride / DNA binding domain binding / macrophage derived foam cell differentiation / positive regulation of vascular associated smooth muscle cell apoptotic process / STAT family protein binding / positive regulation of fatty acid metabolic process / response to lipid / negative regulation of SMAD protein signal transduction / LBD domain binding / negative regulation of type II interferon-mediated signaling pathway / negative regulation of cholesterol storage / E-box binding / alpha-actinin binding / lipid homeostasis / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / monocyte differentiation / negative regulation of macrophage derived foam cell differentiation / negative regulation of blood vessel endothelial cell migration / negative regulation of lipid storage / cellular response to low-density lipoprotein particle stimulus / negative regulation of BMP signaling pathway / white fat cell differentiation / negative regulation of mitochondrial fission / positive regulation of cholesterol efflux / retinoic acid receptor signaling pathway / positive regulation of fat cell differentiation / negative regulation of osteoblast differentiation / cell fate commitment / positive regulation of DNA binding / BMP signaling pathway / long-chain fatty acid transport / nuclear retinoid X receptor binding / regulation of cellular response to insulin stimulus / cell maturation / negative regulation of signaling receptor activity / epithelial cell differentiation / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / hormone-mediated signaling pathway / negative regulation of angiogenesis / response to nutrient / negative regulation of miRNA transcription / negative regulation of MAP kinase activity / fatty acid metabolic process / Regulation of PTEN gene transcription / transcription coregulator binding / peptide binding / negative regulation of smooth muscle cell proliferation / negative regulation of transforming growth factor beta receptor signaling pathway / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / placenta development / regulation of circadian rhythm / lipid metabolic process / PPARA activates gene expression / regulation of blood pressure / positive regulation of DNA-binding transcription factor activity / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / negative regulation of inflammatory response / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / cellular response to insulin stimulus / nuclear receptor activity / activation of cysteine-type endopeptidase activity involved in apoptotic process / : / rhythmic process / glucose homeostasis / cellular response to hypoxia / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / sequence-specific DNA binding / nucleic acid binding / cell differentiation / receptor complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / intracellular membrane-bounded organelle / innate immune response / negative regulation of DNA-templated transcription / chromatin binding
Similarity search - Function
Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Peroxisome proliferator-activated 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 ...Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Peroxisome proliferator-activated 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
Similarity search - Domain/homology
Chem-Y9A / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
Authorsde Paula, K. / Nascimento, A.S.
Funding support Brazil, 5items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2010/15376-8 Brazil
Sao Paulo Research Foundation (FAPESP)2014/06565-2 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)476606/2010-1 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)485950/2013-8 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)303165/2018-9 Brazil
CitationJournal: J.Mol.Graph.Model. / Year: 2021
Title: Tetrazoles as PPAR gamma ligands: A structural and computational investigation.
Authors: de Paula, K. / Santos, J.C. / Mafud, A.C. / Nascimento, A.S.
History
DepositionFeb 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 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

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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)64,0604
Polymers63,4702
Non-polymers5912
Water77543
1
A: Peroxisome proliferator-activated receptor gamma
hetero molecules

B: Peroxisome proliferator-activated receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0604
Polymers63,4702
Non-polymers5912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555x+1/2,y+1/2,z1
Buried area2070 Å2
ΔGint-11 kcal/mol
Surface area23350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.791, 62.142, 118.277
Angle α, β, γ (deg.)90.000, 101.951, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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


Mass: 31734.863 Da / Num. of mol.: 2 / Fragment: UNP residues 232-505
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P37231
#2: Chemical ChemComp-Y9A / ~{N}-[[3-[(4-methylphenyl)methoxy]phenyl]methyl]-1~{H}-1,2,3,4-tetrazol-5-amine


Mass: 295.339 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H17N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.63 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 100 mM HEPES, pH 7.0 and 0.85 M Sodium Citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Oct 11, 2012 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 2.29→49.05 Å / Num. obs: 27930 / % possible obs: 93.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 54.13 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.025 / Rrim(I) all: 0.047 / Net I/σ(I): 10.4
Reflection shellResolution: 2.29→2.37 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.576 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2694 / CC1/2: 0.874 / Rpim(I) all: 0.358 / Rrim(I) all: 0.68 / Χ2: 0.64 / % possible all: 92.9

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SZ1

3sz1


Resolution: 2.29→45.39 Å / SU ML: 0.3031 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.8063
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2592 1299 4.66 %
Rwork0.2025 26580 -
obs0.2051 27879 93.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.39 Å2
Refinement stepCycle: LAST / Resolution: 2.29→45.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3934 0 44 43 4021
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01384062
X-RAY DIFFRACTIONf_angle_d1.45085503
X-RAY DIFFRACTIONf_chiral_restr0.068650
X-RAY DIFFRACTIONf_plane_restr0.01702
X-RAY DIFFRACTIONf_dihedral_angle_d12.9812548
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.380.32631680.28532896X-RAY DIFFRACTION92.57
2.38-2.490.29311300.24752985X-RAY DIFFRACTION94.82
2.49-2.620.29451500.23982990X-RAY DIFFRACTION95.67
2.62-2.790.31621390.22443053X-RAY DIFFRACTION95.8
2.79-30.29241600.22312978X-RAY DIFFRACTION95.9
3-3.30.2951340.22863085X-RAY DIFFRACTION96.7
3.3-3.780.30211330.21522625X-RAY DIFFRACTION83.63
3.78-4.760.20231420.17192807X-RAY DIFFRACTION87.92
4.76-45.390.24131430.18533161X-RAY DIFFRACTION96.81
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)
14.0255510165-1.29828267579-3.194320972364.029328131282.492619891826.79678950805-0.377514007582-0.196248632111-0.0168950189834-0.06234662201780.668000380665-0.2326368020510.01232208274581.20794820039-0.2930137825930.367333761082-0.1213138567590.005339636083520.663024370211-0.07048286417420.467579255657-1.581389505649.11362839984-10.528713585
24.30773129505-0.541967755738-1.353871075752.213189256220.6106434392736.03089845415-0.2344897017130.04815178180920.384447763488-0.1740084264530.198821681733-0.000153451305941-0.93332129092-0.245226939521-0.01280242625930.546705440899-0.0862746921822-0.1128044193480.517213483766-0.008776706871540.485298851631-12.969915786219.3225798621-15.6166411373
32.22111355794-0.5986243171490.4738509079962.241039844681.418493301745.24415451751-0.3099973369820.395614524693-0.419891172623-0.185347955540.1935512474640.4129126861510.203035936595-0.732479618580.09281108142860.447825934238-0.2294685321150.02564951732750.634731963896-0.03481749247560.558897543698-13.53510679186.43929506772-18.1185228541
43.8784747748-3.01595231252-1.590012043242.491748705710.811810559305-0.05854702682290.07544014058310.781409078367-0.133838889225-0.174001165725-0.1640434555830.4388092504660.0598869263443-0.6077701873710.09022859803190.789766934396-0.212251138743-0.1272654294910.800287114770.002714435188890.554674513299-21.715994659916.7371773352-22.0315891614
55.16366716818-2.265620073561.291160837182.85594463592-1.986271878575.149980322480.2092382557250.695464948925-0.602777553921-0.705531109847-0.234963251093-0.04759322036710.838188224117-0.0612212734558-0.1152041134830.710329111936-0.1283432673770.08077259871630.52058422157-0.118862964990.639594592766-25.6020454745-18.5800356182-38.6551573949
61.78738114718-0.288335288169-1.973349955640.47990166742-0.0009489700384675.781314669260.3245136573460.37291702580.3315397645360.511598538825-0.460241348814-0.1566956013060.783350546501-2.237510776680.01241896472011.40893918595-0.0638730908797-0.07715372052031.753576112250.1460455773780.822622408603-46.4284346418-8.33771327769-50.20079011
76.10315689135-0.1654029781111.696521210552.617308409160.9042753939595.410979419670.002555994718990.119333267168-0.423216957936-0.38977996933-0.0739613475951-0.03469572170390.00613154767443-0.3561297472920.06666280318040.486873262134-0.1756111163830.0531693045150.453700628378-0.01622093104660.485915918629-36.7642120779-12.5950706883-27.06208503
87.506457550722.62899372766-3.988834500753.32510963285-0.8472365494992.32367572659-0.3685706554860.279234553771-0.276703932578-0.314279272875-0.1104498311020.02348829549690.125304616016-0.3167061705950.6251662819350.579526128786-0.1735747984910.01387808353640.548078615061-0.04771277767840.538048833592-30.1405862399-8.09299645703-33.8161925739
95.02718878496-1.641624514941.208047369344.68106124271-2.125042916656.37956415101-0.06931597580980.5957256138640.444502461737-0.2506719109550.107324257903-0.0991158019638-1.1239239739-0.503084985452-0.06246552665650.899511664559-0.06856202848290.09957571225460.7002672602960.04199264930570.465069299115-31.3991950466-2.16837616102-44.5282688615
103.47176884219-0.211316991813-1.008736495372.076822879731.772150568175.457384113010.230016022733-0.380758979788-0.465808346829-0.14080187841-0.114966453665-0.539741077305-0.1295557907670.554088128445-0.1156526645150.470745823318-0.1352046865420.02705859054030.446923112618-0.005293095625060.607411327472-19.1241498873-13.0717067089-24.1670109372
112.35269075678-2.64162969085-2.49564301455.442768568220.8272231221415.313214280940.429808039284-0.2426724704630.822023613194-0.3897962518250.1592260701240.0668267974507-1.3965743065-0.179887324887-0.4234027302520.687598539907-0.1195060701670.01357515847970.4457147278060.01001796796770.707314736257-27.89628981750.308137482218-29.7906722268
123.13452107916-0.5042923003712.054397027468.70495776772-5.499024211126.44963483115-0.4387530520890.162230902904-0.0798478050.390305860512-0.02833190333080.536301082553-0.171703642871-0.8309817042320.4772285781180.971712189489-0.09277185145420.2095056362981.18630928822-0.135839038220.858802148485-51.085229005-4.39015533981-30.997897015
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 207 through 246 )AA207 - 2461 - 42
22chain 'A' and (resid 247 through 345 )AA247 - 34543 - 129
33chain 'A' and (resid 346 through 430 )AA346 - 430130 - 214
44chain 'A' and (resid 431 through 476 )AA - B431 - 2215
55chain 'B' and (resid 207 through 251 )BC207 - 2511 - 41
66chain 'B' and (resid 252 through 276 )BC252 - 27642 - 59
77chain 'B' and (resid 277 through 321 )BC277 - 32160 - 104
88chain 'B' and (resid 322 through 333 )BC322 - 333105 - 116
99chain 'B' and (resid 334 through 377 )BC334 - 377117 - 160
1010chain 'B' and (resid 378 through 430 )BC378 - 430161 - 215
1111chain 'B' and (resid 431 through 459 )BC431 - 459216 - 244
1212chain 'B' and (resid 460 through 475 )BC460 - 475245 - 256

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