7PDT | pdb_00007pdt

Crystal structure of a mutated form of RXRalpha ligand binding domain in complex with BMS649 and a coactivator fragment

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
C [auth B]	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8038700	3001442	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8038700	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)
C [auth B]		e7pdtB1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F:	ECOD (v294.1)
A		e7pdtA1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F:	ECOD (v294.1)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth U], D [auth V]	Nuclear receptor coactivator 2	protein binding binding protein domain specific binding molecular function inhibitor activity molecular function regulator activity transcription regulator inhibitor activity DNA binding sequence-specific DNA binding double-stranded DNA binding nucleic acid 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 protein binding binding protein domain specific binding molecular function inhibitor activity molecular function regulator activity transcription regulator inhibitor activity DNA binding sequence-specific DNA binding double-stranded DNA binding nucleic acid 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 transcription coactivator activity transcription regulator activity transcription coregulator activity transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding DNA-binding transcription factor binding RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding intronic transcription regulatory region sequence-specific DNA binding protein dimerization activity signaling receptor binding aryl hydrocarbon receptor binding	regulation of biological process regulation of cellular process regulation of lipid metabolic process biological regulation primary metabolic process metabolic process cellular process regulation of metabolic process lipid metabolic process regulation of primary metabolic process developmental process multicellular organismal process regulation of developmental process connective tissue development regulation of biological process regulation of cellular process regulation of lipid metabolic process biological regulation primary metabolic process metabolic process cellular process regulation of metabolic process lipid metabolic process regulation of primary metabolic process developmental process multicellular organismal process regulation of developmental process connective tissue development adipose tissue development positive regulation of adipose tissue development animal organ development positive regulation of biological process tissue development positive regulation of developmental process regulation of adipose tissue development anatomical structure development positive regulation of multicellular organismal process regulation of multicellular organismal 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 cellular response to stimulus cellular response to endogenous stimulus cellular response to chemical stimulus cellular response to hormone stimulus negative regulation of signaling signaling negative regulation of biological process regulation of signal transduction negative regulation of cell communication cell communication negative regulation of smoothened signaling pathway negative regulation of cellular process signal transduction regulation of smoothened signaling pathway regulation of signaling cell surface receptor signaling pathway negative regulation of response to stimulus negative regulation of signal transduction smoothened signaling pathway regulation of response to stimulus regulation of cell communication regulation of biosynthetic process rhythmic process circadian regulation of gene expression circadian rhythm regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process macromolecule metabolic process RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription intracellular receptor signaling pathway intracellular signal transduction peroxisome proliferator activated receptor signaling pathway nuclear receptor-mediated signaling pathway mRNA transcription by RNA polymerase II mRNA transcription mRNA metabolic process transcription by RNA polymerase II behavior circadian behavior locomotory behavior rhythmic behavior locomotor rhythm response to Thyroglobulin triiodothyronine cellular response to Thyroglobulin triiodothyronine 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 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 positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process monosaccharide metabolic process carbohydrate metabolic process hexose metabolic process regulation of small molecule metabolic process small molecule metabolic process regulation of carbohydrate metabolic process regulation of glucose metabolic process glucose metabolic process	RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure organelle cytoplasm membrane-enclosed lumen intracellular organelle lumen RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure organelle cytoplasm membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen membraneless organelle intracellular membraneless organelle chromatin chromosome nuclear body
A, C [auth B]	Retinoic acid receptor RXR-alpha	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding transcription factor binding transcription coregulator binding protein binding protein-containing complex binding LBD domain binding protein domain specific binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding transcription factor binding transcription coregulator binding protein binding protein-containing complex binding LBD domain binding protein domain specific binding nuclear receptor activity DNA-binding transcription factor activity, RNA polymerase II-specific molecular transducer activity transcription regulator activity DNA-binding transcription factor activity signaling receptor activity ligand-modulated transcription factor activity retinoic acid binding organic acid binding isoprenoid binding retinoid binding ion binding anion binding lipid binding carboxylic acid binding monocarboxylic acid binding small molecule binding identical protein binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding DNA-binding transcription factor binding nuclear vitamin D receptor binding retinoic acid-responsive element binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding RNA polymerase II cis-regulatory region sequence-specific DNA binding nuclear thyroid hormone receptor binding nuclear retinoic acid receptor binding nuclear steroid receptor activity DNA binding domain binding transcription coactivator binding chromatin binding chromatin DNA binding peptide binding RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding intronic transcription regulatory region sequence-specific DNA binding cation binding transition metal ion binding zinc ion binding metal ion binding enzyme binding	cellular response to stimulus catabolic process response to stimulus proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process cellular response to misfolded protein response to misfolded protein cellular response to stress modification-dependent macromolecule catabolic process response to stress protein metabolic process cellular response to topologically incorrect protein primary metabolic process proteasomal protein catabolic process cellular response to stimulus catabolic process response to stimulus proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process cellular response to misfolded protein response to misfolded protein cellular response to stress modification-dependent macromolecule catabolic process response to stress protein metabolic process cellular response to topologically incorrect protein primary metabolic process proteasomal protein catabolic process protein catabolic process nuclear protein quality control by the ubiquitin-proteasome system modification-dependent protein catabolic process response to topologically incorrect protein ubiquitin-dependent protein catabolic process metabolic process cellular process macromolecule metabolic process protein quality control for misfolded or incompletely synthesized proteins developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development heart growth cell population proliferation developmental growth cardiac muscle tissue development cardiac muscle cell proliferation growth organ growth tissue development striated muscle tissue development muscle cell proliferation cardiac muscle tissue growth muscle tissue development striated muscle cell proliferation placenta development mesenchyme development 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 apoptotic process programmed cell death positive regulation of cellular process cellular developmental process cardiac muscle cell differentiation muscle cell differentiation cardiocyte differentiation muscle structure development cell differentiation striated muscle cell differentiation regulation of developmental process regulation of biomineral tissue development regulation of bone mineralization positive regulation of ossification positive regulation of developmental process positive regulation of biomineral tissue development ossification biomineral tissue development regulation of multicellular organismal process regulation of multicellular organismal development bone mineralization positive regulation of bone mineralization positive regulation of multicellular organismal process regulation of ossification intracellular receptor signaling pathway 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 embryo development ending in birth or egg hatching chordate embryonic development embryo development in utero embryonic development heart morphogenesis anatomical structure morphogenesis animal organ morphogenesis multi-multicellular organism process reproductive process maternal process involved in female pregnancy multicellular organismal reproductive process developmental process involved in reproduction maternal placenta development female pregnancy multi-organism reproductive process angiogenesis involved in coronary vascular morphogenesis blood vessel morphogenesis tube development coronary vasculature development angiogenesis vasculature development tube morphogenesis anatomical structure formation involved in morphogenesis coronary vasculature morphogenesis blood vessel development RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process nervous system development cellular response to low-density lipoprotein particle stimulus response to lipoprotein particle cellular response to lipoprotein particle stimulus peroxisome proliferator activated receptor signaling pathway mRNA transcription by RNA polymerase II mRNA transcription mRNA metabolic process transcription by RNA polymerase II myeloid leukocyte differentiation hemopoiesis cell development mononuclear cell differentiation myeloid cell differentiation monocyte differentiation leukocyte differentiation negative regulation of biological process negative regulation of RNA biosynthetic process negative regulation of cellular 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 ventricular cardiac muscle cell differentiation ventricular cardiac muscle tissue morphogenesis ventricular cardiac muscle tissue development cardiac chamber development muscle organ development cardiac chamber morphogenesis muscle tissue morphogenesis tissue morphogenesis cardiac ventricle morphogenesis cardiac muscle tissue morphogenesis cardiac ventricle development muscle organ morphogenesis positive regulation of DNA-templated transcription positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of myelination regulation of nervous system development myelination axon ensheathment ensheathment of neurons sensory organ development eye development visual system development camera-type eye development sensory system development epithelium development visceral serous pericardium development pericardium development response to retinoic acid response to lipid response to oxygen-containing compound response to corticosteroid response to steroid hormone response to glucocorticoid regulation of localization establishment of protein localization regulation of protein localization transport positive regulation of establishment of protein localization positive regulation of protein transport localization intracellular protein localization regulation of lipoprotein transport regulation of transport positive regulation of lipoprotein transport regulation of establishment of protein localization regulation of protein transport lipoprotein transport establishment of localization positive regulation of transport protein transport macromolecule localization positive regulation of protein localization lipoprotein localization anatomical structure maturation cell maturation developmental maturation embryo implantation positive regulation of cell communication regulation of response to nutrient levels positive regulation of signal transduction regulation of signal transduction cellular response to vitamin D response to vitamin D positive regulation of intracellular signal transduction cellular response to oxygen-containing compound cellular response to nutrient levels regulation of response to stimulus cellular response to lipid regulation of vitamin D receptor signaling pathway response to nutrient levels response to vitamin positive regulation of response to stimulus regulation of intracellular signal transduction regulation of signaling response to nutrient vitamin D receptor signaling pathway cellular response to vitamin positive regulation of vitamin D receptor signaling pathway regulation of cell communication cellular response to nutrient positive regulation of signaling negative regulation of cell population proliferation regulation of cell population proliferation regulation of thyroid hormone receptor signaling pathway positive regulation of thyroid hormone receptor signaling pathway thyroid hormone receptor signaling pathway positive regulation of protein metabolic process positive regulation of translation protein biosynthetic process post-transcriptional regulation of gene expression translational initiation regulation of translational initiation by iron regulation of translational initiation regulation of protein metabolic process positive regulation of translational initiation by iron translation positive regulation of gene expression regulation of translation positive regulation of translational initiation negative regulation of gene expression prostate gland development regulation of reproductive process gland development prostate gland epithelium morphogenesis gland morphogenesis reproductive structure development regulation of morphogenesis of an epithelium regulation of anatomical structure morphogenesis regulation of morphogenesis of a branching structure reproductive system development morphogenesis of an epithelium urogenital system development regulation of branching involved in prostate gland morphogenesis prostate gland morphogenesis morphogenesis of a branching structure branching involved in prostate gland morphogenesis morphogenesis of a branching epithelium secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development epithelial cell differentiation prostate glandular acinus development epithelial cell differentiation involved in prostate gland development glandular epithelial cell differentiation columnar/cuboidal epithelial cell differentiation	protein-containing complex transcription regulator complex intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome signaling receptor complex axon cell projection neuron projection protein-containing complex transcription regulator complex intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome signaling receptor complex axon cell projection neuron projection plasma membrane bounded cell projection membrane-bounded organelle mitochondrion cytoplasm intracellular membrane-bounded organelle RNA polymerase II transcription regulator complex nucleus nuclear protein-containing complex membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth U], D [auth V]	IPR010011	Nuclear receptor coactivator, DUF1518	Domain
B [auth U], D [auth V]	IPR009110	Nuclear receptor coactivator, interlocking	Homologous Superfamily
B [auth U], D [auth V]	IPR037077	Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily	Homologous Superfamily
B [auth U], D [auth V]	IPR017426	Nuclear receptor coactivator	Family
B [auth U], D [auth V]	IPR056193	Nuclear receptor coactivator 1-3, bHLH domain	Domain
B [auth U], D [auth V]	IPR014935	Nuclear receptor coactivator, receptor-binding domain	Domain
B [auth U], D [auth V]	IPR013767	PAS fold	Domain
B [auth U], D [auth V]	IPR000014	PAS domain	Domain
B [auth U], D [auth V]	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain	Domain
B [auth U], D [auth V]	IPR014920	Nuclear receptor coactivator, Ncoa-type, interlocking	Domain
B [auth U], D [auth V]	IPR035965	PAS domain superfamily	Homologous Superfamily
B [auth U], D [auth V]	IPR028822	Nuclear receptor coactivator 2, basic helix-loop-helix	Domain
B [auth U], D [auth V]	IPR032565	Nuclear receptor coactivator 2/3, DUF4927	Domain
B [auth U], D [auth V]	IPR036638	Helix-loop-helix DNA-binding domain superfamily	Homologous Superfamily
A, C [auth B]	IPR001628	Zinc finger, nuclear hormone receptor-type	Domain
A, C [auth B]	IPR021780	Nuclear/hormone receptor activator site AF-1	Domain
A, C [auth B]	IPR013088	Zinc finger, NHR/GATA-type	Homologous Superfamily
A, C [auth B]	IPR000003	Retinoid X receptor/HNF4	Family
A, C [auth B]	IPR050274	Nuclear hormone receptor family NR2 subfamily	Family
A, C [auth B]	IPR001723	Nuclear hormone receptor	Family
A, C [auth B]	IPR000536	Nuclear hormone receptor, ligand-binding domain	Domain
A, C [auth B]	IPR035500	Nuclear hormone receptor-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth U], D [auth V]	Pharos: Q15596	breast carcinoma prostate cancer psoriasis ulcerative colitis adenoma endometriosis interstitial cystitis Mammary Neoplasms osteosarcoma testicular cancer atypical teratoid rhabdoid tumor Crohn disease Gaucher disease large cell medulloblastoma pancreatic intraductal papillary-mucinous neoplasm breast carcinoma prostate cancer psoriasis ulcerative colitis adenoma endometriosis interstitial cystitis Mammary Neoplasms osteosarcoma testicular cancer atypical teratoid rhabdoid tumor Crohn disease Gaucher disease large cell medulloblastoma pancreatic intraductal papillary-mucinous neoplasm testicular germ cell tumor breast cancer endogenous depression glioblastoma medulloblastoma plasma cell myeloma