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- PDB-5y7x: Human Peroxisome proliferator-activated receptor (PPAR) delta in ... -

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Basic information

Entry
Database: PDB / ID: 5y7x
TitleHuman Peroxisome proliferator-activated receptor (PPAR) delta in complexed with a potent and selective agonist
ComponentsPeroxisome proliferator-activated receptor delta
KeywordsPROTEIN BINDING / peroxisome proliferator-activated receptor / selenazole / diabetes / pi-sulfur interaction.
Function / homology
Function and homology information


fat cell proliferation / positive regulation of fat cell proliferation / keratinocyte migration / linoleic acid binding / positive regulation of skeletal muscle tissue regeneration / axon ensheathment / regulation of skeletal muscle satellite cell proliferation / glucose transmembrane transport / positive regulation of myoblast proliferation / fatty acid catabolic process ...fat cell proliferation / positive regulation of fat cell proliferation / keratinocyte migration / linoleic acid binding / positive regulation of skeletal muscle tissue regeneration / axon ensheathment / regulation of skeletal muscle satellite cell proliferation / glucose transmembrane transport / positive regulation of myoblast proliferation / fatty acid catabolic process / Carnitine metabolism / negative regulation of myoblast differentiation / Regulation of pyruvate dehydrogenase (PDH) complex / Signaling by Retinoic Acid / nuclear steroid receptor activity / positive regulation of fatty acid metabolic process / cell-substrate adhesion / fatty acid beta-oxidation / negative regulation of cholesterol storage / cellular response to nutrient levels / decidualization / keratinocyte proliferation / positive regulation of fat cell differentiation / fatty acid transport / adipose tissue development / energy homeostasis / embryo implantation / hormone-mediated signaling pathway / cholesterol metabolic process / phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of miRNA transcription / fatty acid metabolic process / generation of precursor metabolites and energy / apoptotic signaling pathway / wound healing / lipid metabolic process / transcription coactivator binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / Nuclear Receptor transcription pathway / glucose metabolic process / nuclear receptor activity / negative regulation of epithelial cell proliferation / sequence-specific double-stranded DNA binding / cellular response to hypoxia / DNA-binding transcription factor binding / cell population proliferation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell differentiation / 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 DNA-templated transcription / lipid binding / apoptotic process / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Peroxisome proliferator-activated receptor, beta / 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 / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors ...Peroxisome proliferator-activated receptor, beta / 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 / 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-8RR / hexyl beta-D-glucopyranoside / : / S-1,2-PROPANEDIOL / Peroxisome proliferator-activated receptor delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.699 Å
AuthorsKim, H.L. / Chin, J.W. / Cho, S.J. / Song, J.Y. / Yoon, H.S. / Bae, J.H.
CitationJournal: To Be Published
Title: Design, synthesis, and the X-ray co-crystal structure of Highly Potent, Selective, and Orally Bioavailable, Novel Peroxisome Proliferator-Activated Receptor delta Agonists
Authors: Chin, J.W. / Cho, S.J.
History
DepositionAug 18, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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 delta
B: Peroxisome proliferator-activated receptor delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,35510
Polymers66,6392
Non-polymers1,7168
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-33 kcal/mol
Surface area24130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.766, 93.896, 96.871
Angle α, β, γ (deg.)90.00, 97.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Peroxisome proliferator-activated receptor delta / PPAR-delta / NUCI / Nuclear hormone receptor 1 / NUC1 / Nuclear receptor subfamily 1 group C member ...PPAR-delta / NUCI / Nuclear hormone receptor 1 / NUC1 / Nuclear receptor subfamily 1 group C member 2 / Peroxisome proliferator-activated receptor beta / PPAR-beta


Mass: 33319.617 Da / Num. of mol.: 2 / Fragment: UNP residues 171-441
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARD, NR1C2, PPARB / Production host: Escherichia coli (E. coli) / References: UniProt: Q03181
#6: Sugar ChemComp-JZR / hexyl beta-D-glucopyranoside / hexyl beta-D-glucoside / hexyl D-glucoside / hexyl glucoside


Type: D-saccharide / Mass: 264.315 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H24O6

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Non-polymers , 5 types, 256 molecules

#2: Chemical ChemComp-8RR / 2-[2-methyl-4-[[4-methyl-2-[4-(trifluoromethyl)phenyl]-1,3-selenazol-5-yl]methylsulfanyl]phenoxy]ethanoic acid


Mass: 500.393 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H18F3NO3SSe
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.67 Å3/Da / Density % sol: 59.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 10% PEG 8000, 40mM Bis-Tris propane pH 8.5, 2.5% 1,2-propanediol, 200mM KCl, 10mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.699→30.8 Å / Num. obs: 76750 / % possible obs: 98.9 % / Redundancy: 4 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 32.5
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.963

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data processing
PHENIXphasing
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5U3R

5u3r


Resolution: 1.699→29.655 Å / SU ML: 0.22 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 27.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2305 3783 4.94 %
Rwork0.2049 --
obs0.2061 76595 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.699→29.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4192 0 104 250 4546
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064386
X-RAY DIFFRACTIONf_angle_d0.795928
X-RAY DIFFRACTIONf_dihedral_angle_d16.2912616
X-RAY DIFFRACTIONf_chiral_restr0.046674
X-RAY DIFFRACTIONf_plane_restr0.005736
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6992-1.72070.36471070.36862271X-RAY DIFFRACTION83
1.7207-1.74340.37081430.35142491X-RAY DIFFRACTION92
1.7434-1.76720.34921340.32842656X-RAY DIFFRACTION97
1.7672-1.79250.30651140.29112750X-RAY DIFFRACTION100
1.7925-1.81920.28191380.28592709X-RAY DIFFRACTION100
1.8192-1.84770.30411500.27372702X-RAY DIFFRACTION100
1.8477-1.8780.31521560.26372707X-RAY DIFFRACTION100
1.878-1.91030.31461560.26222676X-RAY DIFFRACTION100
1.9103-1.94510.31961510.26532688X-RAY DIFFRACTION100
1.9451-1.98250.28641350.25432783X-RAY DIFFRACTION100
1.9825-2.02290.28271550.23152681X-RAY DIFFRACTION100
2.0229-2.06690.23761580.21732681X-RAY DIFFRACTION100
2.0669-2.1150.2631370.22132763X-RAY DIFFRACTION100
2.115-2.16780.26161430.21712699X-RAY DIFFRACTION100
2.1678-2.22640.25871490.22022741X-RAY DIFFRACTION100
2.2264-2.29190.22461580.20892692X-RAY DIFFRACTION100
2.2919-2.36590.26181350.20662750X-RAY DIFFRACTION100
2.3659-2.45040.2231610.21332669X-RAY DIFFRACTION100
2.4504-2.54840.27051560.21282735X-RAY DIFFRACTION100
2.5484-2.66440.26791470.22072742X-RAY DIFFRACTION100
2.6644-2.80470.23181400.21382717X-RAY DIFFRACTION100
2.8047-2.98030.21781350.21142737X-RAY DIFFRACTION100
2.9803-3.21020.24721110.21622774X-RAY DIFFRACTION100
3.2102-3.53270.21291140.19172768X-RAY DIFFRACTION100
3.5327-4.04280.18261300.17742776X-RAY DIFFRACTION100
4.0428-5.08940.17851280.16282768X-RAY DIFFRACTION100
5.0894-29.65950.20871420.18542686X-RAY DIFFRACTION96

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