4DK8 | pdb_00004dk8

Crystal structure of LXR ligand binding domain in complex with partial agonist 5

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8039081	3001442	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8039081	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)
A	SmpA_OmlA	e4dk8A1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: SmpA_OmlA	ECOD (develop294)
C	SmpA_OmlA	e4dk8C1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: SmpA_OmlA	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	Oxysterols receptor LXR-beta	DNA binding binding nucleic acid binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity protein binding signaling receptor binding apolipoprotein A-I receptor binding apolipoprotein receptor binding nuclear receptor activity molecular transducer activity signaling receptor activity ligand-modulated transcription factor activity DNA binding binding nucleic acid binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity protein binding signaling receptor binding apolipoprotein A-I receptor binding apolipoprotein receptor binding nuclear receptor activity molecular transducer activity signaling receptor activity ligand-modulated transcription factor activity DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity ATPase binding enzyme binding sequence-specific DNA 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 chromatin binding chromatin DNA 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 cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule 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 regulation of biosynthetic process regulation of cellular process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process negative regulation of lipid transport negative regulation of biological process negative regulation of transport negative regulation of lipid localization glycerophospholipid metabolic process primary metabolic process phospholipid metabolic process organophosphate metabolic process phosphate-containing compound metabolic process phosphatidylcholine metabolic process glycerolipid metabolic process phosphorus metabolic process phosphatidylcholine acyl-chain remodeling lipid metabolic process oxoacid metabolic process ketone metabolic process regulation of lipid metabolic process lipid biosynthetic process organic acid biosynthetic process organic acid metabolic process carboxylic acid biosynthetic process regulation of primary metabolic process positive regulation of fatty acid biosynthetic 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 monocarboxylic acid biosynthetic process small molecule biosynthetic process carboxylic acid metabolic process fatty acid biosynthetic process regulation of ketone metabolic process positive regulation of lipid biosynthetic process regulation of fatty acid metabolic process regulation of fatty acid biosynthetic process monocarboxylic acid metabolic process regulation of lipid biosynthetic process positive regulation of small molecule metabolic process cellular response to stimulus intracellular receptor signaling pathway response to stimulus signaling response to endogenous stimulus retinoic acid receptor signaling pathway hormone-mediated signaling pathway intracellular signal transduction cell communication cellular response to endogenous stimulus cellular response to chemical stimulus response to hormone response to chemical signal transduction 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 nucleobase-containing compound metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process miRNA transcription regulation of miRNA metabolic process regulation of nucleobase-containing compound metabolic process miRNA metabolic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription regulation of miRNA transcription response to type II interferon response to cytokine regulation of signal transduction 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 regulation of response to 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 regulation of signaling 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 regulation of cell communication negative regulation of innate immune response mRNA transcription by RNA polymerase II mRNA transcription mRNA metabolic process transcription by RNA polymerase II multicellular organismal process regulation of body fluid levels system process digestive system process regulation of system process positive regulation of secretion positive regulation of digestive system process positive regulation of pancreatic juice secretion regulation of multicellular organismal process regulation of biological quality secretion by tissue pancreatic juice secretion secretion regulation of pancreatic juice secretion regulation of digestive system process regulation of secretion body fluid secretion digestion positive regulation of multicellular organismal process establishment of protein localization regulation of protein localization positive regulation of establishment of protein localization positive regulation of secretion by cell protein localization to extracellular region positive regulation of protein transport regulation of secretion by cell secretion by cell secretion of lysosomal enzymes intracellular protein localization regulation of establishment of protein localization establishment of protein localization to extracellular region export from cell regulation of protein transport protein secretion regulation of secretion of lysosomal enzymes positive regulation of protein secretion regulation of protein secretion protein transport positive regulation of protein localization positive regulation of secretion of lysosomal enzymes response to nutrient levels regulation of lipid storage lipid storage nutrient storage 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 transcription by RNA polymerase II developmental process regulation of developmental process cellular developmental process negative regulation of developmental process macrophage derived foam cell differentiation regulation of cell differentiation negative regulation of macrophage derived foam cell differentiation foam cell differentiation cell differentiation regulation of macrophage derived foam cell differentiation negative regulation of cell differentiation cholesterol storage negative regulation of cholesterol storage negative regulation of lipid storage regulation of cholesterol storage regulation of cellular component organization positive regulation of cellular component organization protein-lipid complex organization cellular component organization cellular component biogenesis regulation of protein-containing complex assembly positive regulation of protein-containing complex assembly cellular component assembly positive regulation of high-density lipoprotein particle assembly protein-containing complex assembly cellular component organization or biogenesis plasma lipoprotein particle organization protein-containing complex organization positive regulation of cellular component biogenesis regulation of high-density lipoprotein particle assembly regulation of cellular component biogenesis regulation of plasma lipoprotein particle levels high-density lipoprotein particle assembly plasma lipoprotein particle assembly protein-lipid complex assembly positive regulation of lipid storage negative regulation of inflammatory response regulation of inflammatory response inflammatory response sterol homeostasis chemical homeostasis homeostatic process cholesterol homeostasis lipid homeostasis negative regulation of proteolysis regulation of protein metabolic process regulation of proteolysis proteolysis protein metabolic process negative regulation of protein metabolic process neutral lipid metabolic process neutral lipid biosynthetic process regulation of triglyceride metabolic process positive regulation of triglyceride metabolic process acylglycerol biosynthetic process triglyceride metabolic process triglyceride biosynthetic process regulation of triglyceride biosynthetic process positive regulation of triglyceride biosynthetic process glycerolipid biosynthetic process acylglycerol metabolic process import into cell negative regulation of endocytosis vesicle-mediated transport negative regulation of pinocytosis regulation of endocytosis negative regulation of cellular component organization regulation of vesicle-mediated transport regulation of pinocytosis pinocytosis endocytosis negative regulation of response to endoplasmic reticulum stress regulation of cellular response to stress regulation of response to endoplasmic reticulum stress cellular response to stress response to endoplasmic reticulum stress negative regulation of gene expression negative regulation of cold-induced thermogenesis adaptive thermogenesis multicellular organismal-level homeostasis regulation of cold-induced thermogenesis cold-induced thermogenesis temperature homeostasis negative regulation of multicellular organismal process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex nucleus cellular anatomical structure intracellular anatomical structure cytoplasm cytosol intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
B, D	Nuclear receptor coactivator 1	protein-containing complex binding binding protein binding protein dimerization activity protein-lysine-acetyltransferase activity protein N-acetyltransferase activity catalytic activity, acting on a protein acyltransferase activity N-acetyltransferase activity transferase activity protein N-acyltransferase activity acetyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups catalytic activity protein-containing complex binding binding protein binding protein dimerization activity protein-lysine-acetyltransferase activity protein N-acetyltransferase activity catalytic activity, acting on a protein acyltransferase activity N-acetyltransferase activity transferase activity protein N-acyltransferase activity acetyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups catalytic activity N-acyltransferase activity chromatin binding transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid 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 nuclear estrogen receptor binding	developmental process multicellular organismal process gonad development reproductive system development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics anatomical structure development reproductive structure development developmental process multicellular organismal process gonad development reproductive system development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics anatomical structure development reproductive structure development system development placenta development chordate embryonic development embryonic morphogenesis labyrinthine layer development embryo development in utero embryonic development embryonic placenta morphogenesis labyrinthine layer morphogenesis anatomical structure morphogenesis embryonic placenta development embryo development ending in birth or egg hatching embryonic organ development ovulation cycle rhythmic process estrous cycle multicellular organismal reproductive process response to ketone response to lipid response to stimulus response to hormone response to steroid hormone response to chemical response to endogenous stimulus response to progesterone response to oxygen-containing compound regulation of biological process positive regulation of programmed cell death regulation of cellular process regulation of apoptotic process biological regulation positive regulation of biological process regulation of programmed cell death cell death positive regulation of apoptotic process cellular process apoptotic process programmed cell death positive regulation of cellular process cellular response to stimulus intracellular receptor signaling pathway signaling regulation of signal transduction regulation of thyroid hormone receptor signaling pathway hormone-mediated signaling pathway intracellular signal transduction cell communication cellular response to endogenous stimulus regulation of intracellular signal transduction signal transduction cellular response to hormone stimulus regulation of signaling thyroid hormone receptor signaling pathway cellular response to chemical stimulus regulation of response to stimulus regulation of cell communication nuclear receptor-mediated signaling pathway head development brain development nervous system development cerebellum development central nervous system development metencephalon development hindbrain development behavior male mating behavior reproductive behavior mating behavior forebrain development pallium development cerebral cortex development telencephalon development nuclear receptor-mediated steroid hormone signaling pathway cellular response to steroid hormone stimulus steroid hormone receptor signaling pathway estrogen receptor signaling pathway cellular response to lipid peroxisome proliferator activated receptor signaling pathway mRNA transcription by RNA polymerase II RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression mRNA transcription mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process macromolecule metabolic process regulation of body fluid levels secretion transport mammary gland development gland development establishment of localization body fluid secretion localization lactation regulation of biological quality response to Thyroglobulin triiodothyronine cellular response to Thyroglobulin triiodothyronine progesterone receptor signaling pathway cellular response to nitrogen compound response to peptide hormone cellular response to peptide hormone stimulus response to nitrogen compound regulation of cellular response to insulin stimulus cellular response to oxygen-containing compound response to insulin cellular response to insulin stimulus positive regulation of DNA-templated transcription positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of metabolic process regulation of RNA metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process regulation of gene expression positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process hippocampus development limbic system development regulation of transcription from RNA polymerase II promoter by galactose carbon catabolite regulation of transcription positive regulation of transcription by galactose cellular response to nutrient levels carbon catabolite regulation of transcription from RNA polymerase II promoter carbon catabolite activation of transcription from RNA polymerase II promoter carbon catabolite activation of transcription response to nutrient levels regulation of transcription by galactose response to nutrient positive regulation of transcription from RNA polymerase II promoter by galactose cellular response to nutrient regulation of developmental process connective tissue development adipose tissue development positive regulation of adipose tissue development tissue development positive regulation of developmental process regulation of adipose tissue development positive regulation of multicellular organismal process regulation of multicellular organismal process hypothalamus development diencephalon development response to retinoic acid cellular developmental process regulation of cell differentiation positive regulation of neuron differentiation neurogenesis neuron differentiation positive regulation of cell differentiation cell differentiation generation of neurons regulation of neuron differentiation positive regulation of female receptivity female mating behavior regulation of female receptivity response to estradiol	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex transcription regulator complex intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome RNA polymerase II transcription regulator complex membrane-bounded organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex transcription regulator complex intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome RNA polymerase II transcription regulator complex membrane-bounded organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cell periphery plasma membrane membrane membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR001628	Zinc finger, nuclear hormone receptor-type	Domain
A, C	IPR013088	Zinc finger, NHR/GATA-type	Homologous Superfamily
A, C	IPR023257	Liver X receptor	Family
A, C	IPR050234	Nuclear hormone receptor family NR1 subfamily	Family
A, C	IPR001723	Nuclear hormone receptor	Family
A, C	IPR000536	Nuclear hormone receptor, ligand-binding domain	Domain
A, C	IPR035500	Nuclear hormone receptor-like domain superfamily	Homologous Superfamily
B, D	IPR010011	Nuclear receptor coactivator, DUF1518	Domain
B, D	IPR028819	Nuclear receptor coactivator 1, basic helix-loop-helix	Domain
B, D	IPR009110	Nuclear receptor coactivator, interlocking	Homologous Superfamily
B, D	IPR017426	Nuclear receptor coactivator	Family
B, D	IPR014935	Nuclear receptor coactivator, receptor-binding domain	Domain
B, D	IPR014920	Nuclear receptor coactivator, Ncoa-type, interlocking	Domain
B, D	IPR035965	PAS domain superfamily	Homologous Superfamily
B, D	IPR036638	Helix-loop-helix DNA-binding domain superfamily	Homologous Superfamily
B, D	IPR037077	Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily	Homologous Superfamily
B, D	IPR056193	Nuclear receptor coactivator 1-3, bHLH domain	Domain
B, D	IPR013767	PAS fold	Domain
B, D	IPR000014	PAS domain	Domain
B, D	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C	Pharos: P55055	cholestasis Hepatomegaly psoriasis diabetes mellitus hepatocellular carcinoma primary biliary cholangitis
B, D	Pharos: Q15788	breast carcinoma breast cancer Mammary Neoplasms, Experimental prostate cancer endometriosis ovarian cancer psoriasis adenoma diffuse large B-cell lymphoma glioblastoma malignant glioma astrocytic tumor invasive ductal breast carcinoma osteosarcoma atypical teratoid rhabdoid tumor breast carcinoma breast cancer Mammary Neoplasms, Experimental prostate cancer endometriosis ovarian cancer psoriasis adenoma diffuse large B-cell lymphoma glioblastoma malignant glioma astrocytic tumor invasive ductal breast carcinoma osteosarcoma atypical teratoid rhabdoid tumor cancer large cell medulloblastoma myopathy