3CDS

Crystal structure of the complex between PPAR-gamma and the agonist LT248 (clofibric acid analogue)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d3cdsb_	All alpha proteins	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3cdsa_	All alpha proteins	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8035649	3001442	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8035649	3001442	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	Hormone_recep_1	e3cdsB1	A: alpha arrays	X: Nuclear receptor ligand-binding domain (From Topology)	H: Nuclear receptor ligand-binding domain (From Topology)	T: Nuclear receptor ligand-binding domain	F: Hormone_recep_1	ECOD (1.6)
A	Hormone_recep_1	e3cdsA1	A: alpha arrays	X: Nuclear receptor ligand-binding domain (From Topology)	H: Nuclear receptor ligand-binding domain (From Topology)	T: Nuclear receptor ligand-binding domain	F: Hormone_recep_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.10.565.10	Mainly Alpha	Orthogonal Bundle	Retinoid X Receptor	Retinoid X Receptor	CATH (4.3.0)
A	1.10.565.10	Mainly Alpha	Orthogonal Bundle	Retinoid X Receptor	Retinoid X Receptor	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00104	Ligand-binding domain of nuclear hormone receptor (Hormone_recep)	Ligand-binding domain of nuclear hormone receptor	This all helical domain is involved in binding the hormone in these receptors.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Peroxisome proliferator-activated receptor gamma	binding organic cyclic compound binding nucleic acid binding protein binding WW domain binding protein domain specific binding sequence-specific DNA binding DNA binding LBD domain binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity binding organic cyclic compound binding nucleic acid binding protein binding WW domain binding protein domain specific binding sequence-specific DNA binding DNA binding LBD domain binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity prostanoid receptor activity molecular transducer activity G protein-coupled receptor activity transmembrane signaling receptor activity signaling receptor activity icosanoid receptor activity prostaglandin receptor activity cytoskeletal protein binding alpha-actinin binding actinin binding arachidonate binding fatty acid binding icosanoid binding organic acid binding long-chain fatty acid binding icosatetraenoic acid binding ion binding anion binding lipid binding carboxylic acid binding small molecule binding monocarboxylic acid binding DNA binding domain binding transcription factor binding nuclear retinoic acid receptor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding nuclear retinoid X receptor binding DNA-binding transcription factor binding E-box binding double-stranded DNA binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding SMAD binding R-SMAD binding STAT family protein binding transcription coregulator binding nuclear receptor activity ligand-activated transcription factor activity identical protein binding DNA-binding transcription repressor activity, RNA polymerase II-specific DNA-binding transcription repressor activity chromatin binding peptide binding cation binding transition metal ion binding zinc ion binding metal ion binding enzyme binding	positive regulation of cholesterol efflux regulation of localization transport positive regulation of sterol transport positive regulation of biological process regulation of lipid transport organic hydroxy compound transport localization regulation of cholesterol efflux sterol transport regulation of cholesterol transport positive regulation of cholesterol transport regulation of sterol transport regulation of biological process positive regulation of cholesterol efflux regulation of localization transport positive regulation of sterol transport positive regulation of biological process regulation of lipid transport organic hydroxy compound transport localization regulation of cholesterol efflux sterol transport regulation of cholesterol transport positive regulation of cholesterol transport regulation of sterol transport regulation of biological process regulation of transport biological regulation lipid localization lipid transport positive regulation of lipid localization establishment of localization positive regulation of lipid transport positive regulation of transport regulation of lipid localization macromolecule localization cholesterol transport cholesterol efflux cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling regulation of signal transduction regulation of programmed cell death positive regulation of apoptotic signaling pathway cell communication positive regulation of response to stimulus signal transduction positive regulation of cellular process regulation of signaling positive regulation of programmed cell death regulation of apoptotic process cell death positive regulation of apoptotic process apoptotic signaling pathway regulation of response to stimulus regulation of cell communication cellular process apoptotic process programmed cell death positive regulation of signaling regulation of apoptotic signaling pathway organic anion transport carboxylic acid transport organic acid transport monocarboxylic acid transport fatty acid transport long-chain fatty acid transport intracellular receptor signaling pathway response to endogenous stimulus retinoic acid receptor signaling pathway hormone-mediated signaling pathway intracellular signal transduction cellular response to endogenous stimulus cellular response to chemical stimulus response to hormone response to chemical nuclear receptor-mediated signaling pathway cellular response to hormone stimulus positive regulation of DNA-templated transcription RNA metabolic process positive regulation of miRNA transcription positive regulation of miRNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process positive regulation of metabolic process regulation of RNA metabolic process miRNA transcription positive regulation of biosynthetic process regulation of miRNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process miRNA metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process positive regulation of nucleobase-containing compound metabolic process primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process regulation of miRNA transcription response to type II interferon negative regulation of biological process response to cytokine regulation of type II interferon-mediated signaling pathway response to biotic stimulus cellular response to type II interferon negative regulation of response to type II interferon interferon-mediated signaling pathway cellular response to cytokine stimulus regulation of immune system process immune response response to other organism regulation of innate immune response negative regulation of immune response type II interferon-mediated signaling pathway response to external stimulus regulation of response to cytokine stimulus negative regulation of response to cytokine stimulus defense response to other organism negative regulation of response to external stimulus negative regulation of defense response regulation of immune response regulation of response to type II interferon regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus negative regulation of response to biotic stimulus negative regulation of signaling negative regulation of cell communication cytokine-mediated signaling pathway response to stress regulation of response to stress negative regulation of cellular process innate immune response response to external biotic stimulus negative regulation of type II interferon-mediated signaling pathway cell surface receptor signaling pathway negative regulation of response to stimulus defense response regulation of cytokine-mediated signaling pathway defense response to symbiont negative regulation of signal transduction response to peptide negative regulation of immune system process negative regulation of cytokine-mediated signaling pathway immune system process negative regulation of innate immune response developmental process cellular developmental process cell differentiation cell fate commitment peroxisome proliferator activated receptor signaling pathway mRNA transcription by RNA polymerase II mRNA transcription mRNA metabolic process transcription by RNA polymerase II negative regulation of cell population proliferation cell population proliferation endothelial cell proliferation regulation of vascular endothelial cell proliferation negative regulation of endothelial cell proliferation negative regulation of vascular endothelial cell proliferation regulation of endothelial cell proliferation regulation of cell population proliferation vascular endothelial cell proliferation regulation of epithelial cell proliferation epithelial cell proliferation negative regulation of epithelial cell proliferation negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process positive regulation of molecular function regulation of molecular function positive regulation of low-density lipoprotein receptor activity regulation of vascular associated smooth muscle cell proliferation regulation of smooth muscle cell proliferation negative regulation of vascular associated smooth muscle cell proliferation smooth muscle cell proliferation negative regulation of smooth muscle cell proliferation muscle cell proliferation vascular associated smooth muscle cell proliferation oxoacid metabolic process ketone metabolic process regulation of lipid metabolic process organic acid metabolic process regulation of small molecule metabolic process positive regulation of lipid metabolic process small molecule metabolic process positive regulation of fatty acid metabolic process fatty acid metabolic process carboxylic acid metabolic process regulation of ketone metabolic process regulation of fatty acid metabolic process monocarboxylic acid metabolic process positive regulation of small molecule metabolic process lipid metabolic process rhythmic process circadian rhythm regulation of circadian rhythm chemical homeostasis homeostatic process lipid homeostasis negative regulation of extracellular matrix organization regulation of cellular component organization negative regulation of cellular component organization extracellular matrix organization regulation of cellular component biogenesis cellular component organization cellular component biogenesis cellular component assembly regulation of extracellular matrix assembly negative regulation of extracellular matrix assembly cellular component organization or biogenesis regulation of extracellular matrix organization extracellular matrix assembly extracellular structure organization external encapsulating structure organization negative regulation of inflammatory response regulation of inflammatory response inflammatory response anatomical structure maturation anatomical structure development cell development cell maturation developmental maturation negative regulation of miRNA transcription negative regulation of miRNA metabolic process negative regulation of intracellular signal transduction regulation of intracellular signal transduction intracellular signaling cassette regulation of MAPK cascade MAPK cascade negative regulation of MAPK cascade cell surface receptor signaling pathway via STAT negative regulation of receptor signaling pathway via STAT regulation of receptor signaling pathway via STAT cellular response to nitrogen compound response to peptide hormone response to oxygen-containing compound cellular response to peptide hormone stimulus response to nitrogen compound cellular response to oxygen-containing compound response to insulin cellular response to insulin stimulus multicellular organismal process regulation of developmental process angiogenesis regulation of vasculature development multicellular organism development tube morphogenesis regulation of multicellular organismal process regulation of anatomical structure morphogenesis system development blood vessel development regulation of multicellular organismal development blood vessel morphogenesis tube development negative regulation of blood vessel morphogenesis negative regulation of developmental process negative regulation of angiogenesis vasculature development circulatory system development negative regulation of vasculature development anatomical structure morphogenesis regulation of angiogenesis anatomical structure formation involved in morphogenesis negative regulation of multicellular organismal process muscle cell apoptotic process positive regulation of smooth muscle cell apoptotic process smooth muscle cell apoptotic process regulation of muscle cell apoptotic process regulation of smooth muscle cell apoptotic process positive regulation of muscle cell apoptotic process vascular associated smooth muscle cell apoptotic process positive regulation of vascular associated smooth muscle cell apoptotic process regulation of vascular associated smooth muscle cell apoptotic process negative regulation of gene expression cellular response to growth factor stimulus regulation of cellular response to transforming growth factor beta stimulus cellular response to transforming growth factor beta stimulus regulation of cellular response to growth factor stimulus negative regulation of cellular response to growth factor stimulus negative regulation of cellular response to transforming growth factor beta stimulus response to transforming growth factor beta response to growth factor mitochondrion organization organelle fission mitochondrial fission regulation of organelle organization organelle organization negative regulation of organelle organization negative regulation of mitochondrial fission regulation of mitochondrial fission regulation of mitochondrion organization system process circulatory system process regulation of blood pressure regulation of biological quality blood circulation placenta development animal organ development positive regulation of gene expression response to decreased oxygen levels cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels cellular response to stress response to hypoxia response to oxygen levels response to abiotic stimulus epithelium development tissue development epithelial cell differentiation cell surface receptor protein serine/threonine kinase signaling pathway regulation of transmembrane receptor protein serine/threonine kinase signaling pathway negative regulation of BMP signaling pathway BMP signaling pathway enzyme-linked receptor protein signaling pathway cellular response to BMP stimulus regulation of BMP signaling pathway response to BMP transforming growth factor beta receptor superfamily signaling pathway negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway lipid storage negative regulation of lipid localization maintenance of location regulation of lipid storage negative regulation of lipid storage SMAD protein signal transduction regulation of SMAD protein signal transduction negative regulation of SMAD protein signal transduction protein localization establishment of protein localization cellular localization nitrogen compound transport lipoprotein transport protein transport cellular macromolecule localization lipoprotein localization negative regulation of transforming growth factor beta receptor signaling pathway regulation of transforming growth factor beta receptor signaling pathway transforming growth factor beta receptor signaling pathway negative regulation of locomotion regulation of cell motility regulation of blood vessel endothelial cell migration endothelial cell migration negative regulation of endothelial cell migration negative regulation of blood vessel endothelial cell migration regulation of locomotion regulation of cell migration blood vessel endothelial cell migration regulation of endothelial cell migration negative regulation of cell motility cell migration cell motility locomotion negative regulation of cell migration cellular response to low-density lipoprotein particle stimulus response to lipoprotein particle cellular response to lipoprotein particle stimulus negative regulation of connective tissue replacement involved in inflammatory response wound healing negative regulation of tissue remodeling wound healing involved in inflammatory response negative regulation of connective tissue replacement regulation of connective tissue replacement involved in inflammatory response wound healing connective tissue replacement response to wounding wound healing connective tissue replacement involved in inflammatory response wound healing regulation of tissue remodeling inflammatory response to wounding tissue remodeling regulation of connective tissue replacement myeloid leukocyte differentiation hemopoiesis mononuclear cell differentiation myeloid cell differentiation monocyte differentiation leukocyte differentiation response to lipid fat cell differentiation positive regulation of fat cell differentiation regulation of cell differentiation positive regulation of developmental process positive regulation of cell differentiation regulation of fat cell differentiation regulation of cellular response to insulin stimulus positive regulation of transcription by RNA polymerase II glucose homeostasis carbohydrate homeostasis white fat cell differentiation macrophage derived foam cell differentiation negative regulation of macrophage derived foam cell differentiation foam cell differentiation regulation of macrophage derived foam cell differentiation negative regulation of cell differentiation connective tissue development adipose tissue development positive regulation of adipose tissue development regulation of adipose tissue development positive regulation of multicellular organismal process cholesterol storage negative regulation of cholesterol storage regulation of cholesterol storage regulation of osteoblast differentiation negative regulation of osteoblast differentiation osteoblast differentiation ossification regulation of adiponectin secretion positive regulation of establishment of protein localization positive regulation of adiponectin secretion adiponectin secretion regulation of hormone levels establishment of protein localization to extracellular region protein secretion regulation of protein secretion regulation of secretion endocrine hormone secretion positive regulation of protein localization regulation of hormone secretion regulation of protein localization positive regulation of secretion by cell hormone secretion protein localization to extracellular region positive regulation of protein transport secretion by cell regulation of secretion by cell positive regulation of hormone secretion positive regulation of secretion signal release secretion regulation of establishment of protein localization export from cell cell-cell signaling regulation of protein transport positive regulation of protein secretion endocrine process regulation of cellular localization hormone transport regulation of signaling receptor activity negative regulation of molecular function negative regulation of signaling receptor activity sequestering of triglyceride negative regulation of sequestering of triglyceride regulation of sequestering of triglyceride negative regulation of muscle adaptation striated muscle adaptation negative regulation of muscle hypertrophy regulation of system process regulation of muscle hypertrophy regulation of cardiac muscle hypertrophy in response to stress muscle adaptation cardiac muscle adaptation cardiac muscle hypertrophy cardiac muscle hypertrophy in response to stress muscle hypertrophy regulation of muscle adaptation negative regulation of cardiac muscle hypertrophy in response to stress striated muscle hypertrophy regulation of muscle system process muscle system process regulation of cardiac muscle hypertrophy negative regulation of cardiac muscle adaptation regulation of cardiac muscle adaptation negative regulation of cardiac muscle hypertrophy muscle hypertrophy in response to stress response to nutrient levels response to nutrient	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex receptor complex membrane-bounded organelle intracellular organelle organelle intracellular membrane-bounded organelle membraneless organelle intracellular membraneless organelle chromatin chromosome cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex receptor complex membrane-bounded organelle intracellular organelle organelle intracellular membrane-bounded organelle membraneless organelle intracellular membraneless organelle chromatin chromosome RNA polymerase II transcription regulator complex nucleus nuclear protein-containing complex transcription regulator complex membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR001628	Zinc finger, nuclear hormone receptor-type	Domain
A, B	IPR013088	Zinc finger, NHR/GATA-type	Homologous Superfamily
A, B	IPR001723	Nuclear hormone receptor	Family
A, B	IPR003077	Peroxisome proliferator-activated receptor gamma	Family
A, B	IPR000536	Nuclear hormone receptor, ligand-binding domain	Domain
A, B	IPR003074	Peroxisome proliferator-activated receptor	Family
A, B	IPR050234	Nuclear hormone receptor family NR1 subfamily	Family
A, B	IPR022590	Peroxisome proliferator-activated receptor gamma, N-terminal	Domain
A, B	IPR035500	Nuclear hormone receptor-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P37231	familial partial lipodystrophy type 2 diabetes mellitus obesity disorder psoriasis Barrett esophagus glomerulonephritis atherosclerosis Crohn disease diabetes mellitus hypertensive disorder melanoma colorectal cancer Alzheimer disease Diabetes Mellitus, Experimental metabolic disease familial partial lipodystrophy type 2 diabetes mellitus obesity disorder psoriasis Barrett esophagus glomerulonephritis atherosclerosis Crohn disease diabetes mellitus hypertensive disorder melanoma colorectal cancer Alzheimer disease Diabetes Mellitus, Experimental metabolic disease leukostasis giant cell glioblastoma acute lung injury congestive heart failure ulcerative colitis antiphospholipid syndrome PPARG-related familial partial lipodystrophy autosomal dominant polycystic kidney disease malignant pancreatic neoplasm monogenic obesity kidney failure ACTH-dependent Cushing syndrome thyroid adenoma non-alcoholic fatty liver disease adenocarcinoma granular cell carcinoma tubular adenocarcinoma liver disease malignant colon neoplasm T-cell non-Hodgkin lymphoma thyroid gland carcinoma gliosarcoma liver cancer autoimmune disease malignant ependymoma ileocolitis diabetic kidney disease breast fibroadenoma maturity-onset diabetes of the young ductal breast carcinoma in situ esophageal adenocarcinoma kidney disease acquired metabolic disease large cell medulloblastoma colon carcinoma acute kidney failure colorectal carcinoma thyroid gland papillary carcinoma lipodystrophy tuberculosis cribriform carcinoma of breast pancreatic intraductal papillary-mucinous neoplasm lung adenocarcinoma polycystic kidney disease 2 hepatocellular carcinoma lysosomal lipid storage disorder cutaneous melanoma hyperinsulinism malignant glioma primitive neuroectodermal tumor benign colon neoplasm inherited lipid metabolism disorder medulloblastoma interstitial cystitis cerebrovascular disorder subarachnoid hemorrhage ischemia reperfusion injury colonic neoplasm gastric cancer thyroid cancer, nonmedullary, 2 lipoatrophic diabetes osteoarthritis glioma susceptibility 1 coronary artery disease osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia heart failure lung cancer hereditary diffuse gastric adenocarcinoma arteriosclerosis disorder prediabetes syndrome atopic eczema inborn carbohydrate metabolic disorder breast carcinoma MALT lymphoma pustulosis palmaris et plantaris cancer schizophrenia invasive ductal breast carcinoma ischemic disease neurodegenerative disease thyroid cancer leprosy non-small cell lung carcinoma gastric neoplasm congenital generalized lipodystrophy osteoarthritis susceptibility 1 cribriform carcinoma pancreatic intraductal papillary-mucinous carcinoma Hashimoto thyroiditis liver neoplasm Crohn's colitis pancreatic neoplasm lung carcinoma Cushing disease due to pituitary adenoma hyperglycemia

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.