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- PDB-2q5g: Ligand binding domain of PPAR delta receptor in complex with a pa... -

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Basic information

Entry
Database: PDB / ID: 2q5g
TitleLigand binding domain of PPAR delta receptor in complex with a partial agonist
ComponentsPeroxisome proliferator-activated receptor delta
KeywordsTRANSCRIPTION / PPAR delta
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 / regulation of skeletal muscle satellite cell proliferation / axon ensheathment / 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 / regulation of skeletal muscle satellite cell proliferation / axon ensheathment / glucose transmembrane transport / positive regulation of myoblast proliferation / fatty acid catabolic process / negative regulation of myoblast differentiation / Carnitine metabolism / Regulation of pyruvate dehydrogenase (PDH) complex / Signaling by Retinoic Acid / nuclear steroid receptor activity / fatty acid beta-oxidation / positive regulation of fatty acid metabolic process / cell-substrate adhesion / 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 / cholesterol metabolic process / hormone-mediated signaling pathway / fatty acid metabolic process / negative regulation of miRNA transcription / phosphatidylinositol 3-kinase/protein kinase B signal transduction / generation of precursor metabolites and energy / apoptotic signaling pathway / wound healing / lipid metabolic process / transcription coactivator binding / negative regulation of inflammatory response / DNA-binding transcription repressor activity, RNA polymerase II-specific / 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 / cell differentiation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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 / chromatin / positive regulation of gene expression / 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-1FA / Peroxisome proliferator-activated receptor delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsPettersson, I. / Sauerberg, P. / Johansson, E. / Hoffman, I. / Tari, L.W. / Hunter, M.J. / Nix, J.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2007
Title: Design of a partial PPARdelta agonist.
Authors: Pettersson, I. / Ebdrup, S. / Havranek, M. / Pihera, P. / Korinek, M. / Mogensen, J.P. / Jeppesen, C.B. / Johansson, E. / Sauerberg, P.
History
DepositionJun 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)66,1704
Polymers64,9852
Non-polymers1,1852
Water0
1
A: Peroxisome proliferator-activated receptor delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0852
Polymers32,4931
Non-polymers5931
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Peroxisome proliferator-activated receptor delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0852
Polymers32,4931
Non-polymers5931
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
A: Peroxisome proliferator-activated receptor delta
B: Peroxisome proliferator-activated receptor delta
hetero molecules

A: Peroxisome proliferator-activated receptor delta
B: Peroxisome proliferator-activated receptor delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,3418
Polymers129,9704
Non-polymers2,3714
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area10750 Å2
ΔGint-91 kcal/mol
Surface area44490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.577, 65.603, 101.149
Angle α, β, γ (deg.)90.00, 124.05, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Peroxisome proliferator-activated receptor delta / / PPAR-delta / PPAR- beta / Nuclear hormone receptor 1 / NUC1 / NUCI


Mass: 32492.588 Da / Num. of mol.: 2 / Fragment: LIGAND BINDING DOMAIN
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
#2: Chemical ChemComp-1FA / [(7-{[2-(3-MORPHOLIN-4-YLPROP-1-YN-1-YL)-6-{[4-(TRIFLUOROMETHYL)PHENYL]ETHYNYL}PYRIDIN-4-YL]THIO}-2,3-DIHYDRO-1H-INDEN- 4-YL)OXY]ACETIC ACID / {7-[2-(3-MORPHOLIN-4-YL-PROP-1-YNYL)-6-(4-TRIFLUOROMETHYL-PHENYLETHYNYL) -PYRIDIN-4-YLSULFANYL]-INDAN-4-YLOXY}-ACETIC ACID


Mass: 592.628 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H27F3N2O4S

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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: 2.49 Å3/Da / Density % sol: 50.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 4, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→53.73 Å / Num. obs: 16233 / % possible obs: 95.7 % / Redundancy: 2.53 % / Rmerge(I) obs: 0.099 / Χ2: 0.97 / Net I/σ(I): 6.3 / Scaling rejects: 1272
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.7-2.82.470.3732.1418216451.1798.6
2.8-2.912.480.3252.4419316391.1297.9
2.91-3.042.470.2683416416271.0997.3
3.04-3.22.470.2173.8426416491.1797
3.2-3.42.520.1614.6424916381.0196.9
3.4-3.662.550.1185.7426216360.8696.4
3.66-4.032.560.0927.4427516290.8995.4
4.03-4.622.60.0719.5428516140.7794.9
4.62-5.812.610.0710421615770.8693.4
5.81-53.732.610.04713.8429915790.8489.3

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Processing

Software
NameVersionClassificationNB
d*TREK9.4LDzdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
d*TREKdata reduction
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GWX

2gwx


Resolution: 2.7→53.73 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.858 / SU B: 15.054 / SU ML: 0.307 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.428 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.305 826 5.1 %RANDOM
Rwork0.225 ---
obs0.229 16225 95.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.635 Å2
Baniso -1Baniso -2Baniso -3
1-2.2 Å20 Å2-0.67 Å2
2--0.16 Å20 Å2
3----3.12 Å2
Refinement stepCycle: LAST / Resolution: 2.7→53.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3792 0 84 0 3876
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223961
X-RAY DIFFRACTIONr_angle_refined_deg1.6251.9825363
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1655472
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.51724.046173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.93815669
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5161520
X-RAY DIFFRACTIONr_chiral_restr0.1030.2611
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022936
X-RAY DIFFRACTIONr_nbd_refined0.2290.21849
X-RAY DIFFRACTIONr_nbtor_refined0.3140.22724
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2112
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1080.24
X-RAY DIFFRACTIONr_mcbond_it0.84622444
X-RAY DIFFRACTIONr_mcangle_it1.4362.53846
X-RAY DIFFRACTIONr_scbond_it1.53231739
X-RAY DIFFRACTIONr_scangle_it2.4764.51517
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.47 61 -
Rwork0.312 1144 -
obs-1205 98.37 %

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