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- PDB-2npa: the crystal structure of the human PPARaplpha ligand binding doma... -

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Basic information

Entry
Database: PDB / ID: 2npa
Titlethe crystal structure of the human PPARaplpha ligand binding domain in complex with a a-hydroxyimino phenylpropanoic acid
Components
  • Peroxisome proliferator-activated receptor alpha
  • SRC- peptide from Nuclear receptor coactivator 1
KeywordsTRANSCRIPTION / protein-agonist complex
Function / homology
Function and homology information


positive regulation of transformation of host cell by virus / regulation of fatty acid transport / enamel mineralization / negative regulation of cell growth involved in cardiac muscle cell development / cellular response to fructose stimulus / regulation of ketone metabolic process / regulation of fatty acid metabolic process / negative regulation of appetite / positive regulation of fatty acid beta-oxidation / lipoprotein metabolic process ...positive regulation of transformation of host cell by virus / regulation of fatty acid transport / enamel mineralization / negative regulation of cell growth involved in cardiac muscle cell development / cellular response to fructose stimulus / regulation of ketone metabolic process / regulation of fatty acid metabolic process / negative regulation of appetite / positive regulation of fatty acid beta-oxidation / lipoprotein metabolic process / positive regulation of fatty acid oxidation / behavioral response to nicotine / negative regulation of hepatocyte apoptotic process / negative regulation of leukocyte cell-cell adhesion / mitogen-activated protein kinase kinase kinase binding / labyrinthine layer morphogenesis / positive regulation of transcription from RNA polymerase II promoter by galactose / regulation of thyroid hormone receptor signaling pathway / positive regulation of female receptivity / ubiquitin conjugating enzyme binding / negative regulation of glycolytic process / positive regulation of fatty acid metabolic process / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / DNA-binding transcription activator activity / nuclear steroid receptor activity / hypothalamus development / male mating behavior / positive regulation of ATP biosynthetic process / NFAT protein binding / negative regulation of cholesterol storage / cellular response to Thyroglobulin triiodothyronine / negative regulation of macrophage derived foam cell differentiation / Synthesis of bile acids and bile salts / epidermis development / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear retinoid X receptor binding / phosphatase binding / response to retinoic acid / positive regulation of lipid biosynthetic process / progesterone receptor signaling pathway / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / cellular response to hormone stimulus / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / Recycling of bile acids and salts / histone acetyltransferase / estrous cycle / intracellular receptor signaling pathway / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / negative regulation of reactive oxygen species biosynthetic process / estrogen receptor signaling pathway / nitric oxide metabolic process / negative regulation of blood pressure / positive regulation of adipose tissue development / hormone-mediated signaling pathway / : / MDM2/MDM4 family protein binding / lactation / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / response to nutrient / negative regulation of cytokine production involved in inflammatory response / positive regulation of gluconeogenesis / positive regulation of neuron differentiation / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cerebellum development / BMAL1:CLOCK,NPAS2 activates circadian expression / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / hippocampus development / response to progesterone / cellular response to starvation / nuclear receptor binding / gluconeogenesis / fatty acid metabolic process / RNA polymerase II transcription regulatory region sequence-specific DNA binding / nuclear estrogen receptor binding / response to insulin / SUMOylation of intracellular receptors / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression
Similarity search - Function
Peroxisome proliferator-activated receptor alpha / Nuclear receptor coactivator 1 / Peroxisome proliferator-activated receptor / 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 ...Peroxisome proliferator-activated receptor alpha / Nuclear receptor coactivator 1 / Peroxisome proliferator-activated receptor / 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 / Nuclear receptor coactivators bHLH domain / PAS domain / Nuclear receptor coactivator, interlocking / : / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / Retinoid X Receptor / Retinoid X Receptor / PAS domain superfamily / 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-MMB / Peroxisome proliferator-activated receptor alpha / Nuclear receptor coactivator 1 / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKim, K.H. / Chung, H.K. / Han, H.O. / Kim, S.H. / Koh, J.S. / Kim, G.T.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2007
Title: Design and synthesis of oxime ethers of alpha-acyl-beta-phenylpropanoic acids as PPAR dual agonists
Authors: Han, H.O. / Kim, S.H. / Kim, K.H. / Hur, G.C. / Yim, H.J. / Chung, H.K. / Woo, S.H. / Koo, K.D. / Lee, C.S. / Koh, J.S. / Kim, G.T.
History
DepositionOct 26, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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 alpha
B: SRC- peptide from Nuclear receptor coactivator 1
C: Peroxisome proliferator-activated receptor alpha
D: SRC- peptide from Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5976
Polymers64,7244
Non-polymers8732
Water5,062281
1
A: Peroxisome proliferator-activated receptor alpha
B: SRC- peptide from Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7983
Polymers32,3622
Non-polymers4371
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Peroxisome proliferator-activated receptor alpha
D: SRC- peptide from Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7983
Polymers32,3622
Non-polymers4371
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.909, 100.074, 61.311
Angle α, β, γ (deg.)90.000, 100.140, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Peroxisome proliferator-activated receptor alpha / PPAR-alpha


Mass: 30513.596 Da / Num. of mol.: 2 / Fragment: ligand binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q07869
#2: Protein/peptide SRC- peptide from Nuclear receptor coactivator 1 / SRC- peptide from steroid receptor coactivator


Mass: 1848.177 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: chemically synthesized 21 mer portion of the human SRC-1
References: UniProt: Q2T9G5, UniProt: Q15788*PLUS
#3: Chemical ChemComp-MMB / (2R,3E)-2-{4-[(5-METHYL-2-PHENYL-1,3-OXAZOL-4-YL)METHOXY]BENZYL}-3-(PROPOXYIMINO)BUTANOIC ACID / (R,E)-2-(4-((5-METHYL-2-PHENYLOXAZOL-4-YL)METHOXY)BENZYL)-3-(PROPOXYIMINO)BUTANOIC ACID


Mass: 436.500 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H28N2O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.79 Å3/Da / Density % sol: 55.98 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: 6% PEG 10K. 0.1M Hepes, 6% ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.54 Å
DetectorType: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Feb 20, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 31665 / Num. obs: 29916 / % possible obs: 95.9 % / Rmerge(I) obs: 0.059 / Χ2: 1.434 / Net I/σ(I): 18.1
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
2.3-2.340.37615121.1697.4
2.34-2.380.3115341.17698.5
2.38-2.430.28315481.19398.9
2.43-2.480.22815111.10698.8
2.48-2.530.21915221.29597.9
2.53-2.590.20415281.26498.4
2.59-2.650.1815191.31998.2
2.65-2.730.14515101.42797.5
2.73-2.810.12515071.52997.4
2.81-2.90.11515221.70997.7
2.9-30.09715091.69496.6
3-3.120.08514991.65696.9
3.12-3.260.07715071.77496
3.26-3.430.06614911.83395.5
3.43-3.650.06214871.9395.8
3.65-3.930.05614731.7894.1
3.93-4.320.04814681.55893.4
4.32-4.930.04514481.32592.8
4.93-6.180.04114541.0891.8
6.18-200.0313670.79585.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K7L

1k7l


Resolution: 2.3→20 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.26 2323 7.3 %RANDOM
Rwork0.22 ---
all-31665 --
obs-29052 91.7 %-
Solvent computationBsol: 52.306 Å2
Displacement parametersBiso mean: 46.979 Å2
Baniso -1Baniso -2Baniso -3
1--1.972 Å20 Å24.416 Å2
2---0.694 Å20 Å2
3---2.666 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4452 0 64 281 4797
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2258.param
X-RAY DIFFRACTION3water_rep.param

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