4WHF | pdb_00004whf

Crystal Structure of TR3 LBD in complex with 1-(3,4,5-trihydroxyphenyl)decan-1-one

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)
A [auth B]	d4whfb_	All alpha proteins	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	Orphan nuclear receptor NR4A1	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth A]	d4whfa_	All alpha proteins	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	Orphan nuclear receptor NR4A1	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)
A [auth B]	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8036433	3001442	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8036433	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 [auth B]		e4whfB1	A: alpha bundles	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: RNA polymerase I subunits A49/A34.5 dimerization domains	F:	ECOD (develop294)
B [auth A]		e4whfA1	A: alpha bundles	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: RNA polymerase I subunits A49/A34.5 dimerization domains	F:	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth B]	1.10.565.10	Mainly Alpha	Orthogonal Bundle	Retinoid X Receptor	Retinoid X Receptor	CATH (4.3.0)
B [auth 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 [auth B], B [auth A]	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 [auth B], B [auth A]	Nuclear receptor subfamily 4 group A member 1	transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding protein binding binding nuclear glucocorticoid receptor binding DNA-binding transcription factor binding 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 factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding protein binding binding nuclear glucocorticoid receptor binding DNA-binding transcription factor binding 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 protein heterodimerization activity protein dimerization activity lipid binding lipopolysaccharide binding carbohydrate derivative binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity nuclear receptor activity molecular transducer activity signaling receptor activity ligand-modulated transcription factor activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity identical protein binding	biological process involved in interspecies interaction between organisms response to stimulus detection of external biotic stimulus response to lipid response to other organism detection of lipopolysaccharide response to oxygen-containing compound response to external stimulus detection of molecule of bacterial origin detection of biotic stimulus response to lipopolysaccharide response to biotic stimulus detection of stimulus response to bacterium response to chemical biological process involved in interspecies interaction between organisms response to stimulus detection of external biotic stimulus response to lipid response to other organism detection of lipopolysaccharide response to oxygen-containing compound response to external stimulus detection of molecule of bacterial origin detection of biotic stimulus response to lipopolysaccharide response to biotic stimulus detection of stimulus response to bacterium response to chemical detection of chemical stimulus response to external biotic stimulus response to molecule of bacterial origin cellular response to stimulus cellular response to nitrogen compound response to corticotropin-releasing hormone response to endogenous stimulus response to peptide hormone cellular response to peptide hormone stimulus response to nitrogen compound cellular response to oxygen-containing compound cellular response to endogenous stimulus cellular response to chemical stimulus response to hormone cellular process cellular response to corticotropin-releasing hormone stimulus cellular response to hormone stimulus regulation of biological process cell population proliferation regulation of cellular process regulation of cell population proliferation regulation of type B pancreatic cell proliferation type B pancreatic cell proliferation biological regulation regulation of epithelial cell proliferation epithelial cell proliferation cell chemotaxis chemotaxis endothelial cell migration taxis cell migration endothelial cell chemotaxis cell motility locomotion RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process macromolecule metabolic process apoptotic process cell death programmed cell death negative regulation of cellular process negative regulation of biological process negative regulation of cell cycle cell cycle regulation of cell cycle positive regulation of programmed cell death regulation of apoptotic process positive regulation of biological process regulation of programmed cell death positive regulation of apoptotic process positive regulation of cellular process developmental process multicellular organismal process cell migration involved in sprouting angiogenesis blood vessel morphogenesis tube development angiogenesis sprouting angiogenesis vasculature development circulatory system development anatomical structure morphogenesis multicellular organism development tube morphogenesis anatomical structure formation involved in morphogenesis anatomical structure development blood vessel endothelial cell migration blood vessel development system development establishment of protein localization cellular localization nucleocytoplasmic transport transport nuclear transport intracellular transport protein localization to nucleus establishment of localization localization import into nucleus establishment of protein localization to organelle protein transport establishment of localization in cell macromolecule localization protein localization to organelle protein import into nucleus intracellular protein localization intracellular protein transport skeletal muscle cell differentiation cellular developmental process skeletal muscle tissue development animal organ development tissue development striated muscle tissue development muscle structure development skeletal muscle organ development cell differentiation muscle tissue development muscle organ development response to fibroblast growth factor cellular response to growth factor stimulus response to growth factor cellular response to fibroblast growth factor stimulus signaling signal transduction cell communication fat cell differentiation cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular component organization or biogenesis non-canonical inflammasome complex assembly defense response response to stress inflammatory response regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of biosynthetic process regulation of macromolecule metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process macrophage activation immune system process cell activation myeloid leukocyte activation leukocyte activation positive regulation of cell population proliferation endothelial cell proliferation positive regulation of epithelial cell proliferation regulation of endothelial cell proliferation positive regulation of endothelial cell proliferation 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 cellular response to vascular endothelial growth factor stimulus	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule nuclear body nucleoplasm organelle lumen membraneless organelle supramolecular complex nuclear ribonucleoprotein granule nuclear lumen nuclear membrane membrane endomembrane system organelle envelope nuclear envelope organelle membrane cytosol protein-containing complex transcription regulator complex chromatin chromosome nucleolus fibrillar center

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B], B [auth A]	IPR001628	Zinc finger, nuclear hormone receptor-type	Domain
A [auth B], B [auth A]	IPR001723	Nuclear hormone receptor	Family
A [auth B], B [auth A]	IPR013088	Zinc finger, NHR/GATA-type	Homologous Superfamily
A [auth B], B [auth A]	IPR003070	Nuclear receptor subfamily 4 group A member 1-3	Family
A [auth B], B [auth A]	IPR003071	Nuclear receptor subfamily 4 group A member 1	Family
A [auth B], B [auth A]	IPR000536	Nuclear hormone receptor, ligand-binding domain	Domain
A [auth B], B [auth A]	IPR035500	Nuclear hormone receptor-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth B], B [auth A]	Pharos: P22736	proteinuria kidney disease malignant pancreatic neoplasm Insulin Resistance lung adenocarcinoma endometriosis myocardial ischemia pancreatic ductal adenocarcinoma adrenal cortex carcinoma breast cancer Duchenne muscular dystrophy exocrine pancreatic carcinoma hepatocellular carcinoma lung carcinoma non-small cell lung carcinoma proteinuria kidney disease malignant pancreatic neoplasm Insulin Resistance lung adenocarcinoma endometriosis myocardial ischemia pancreatic ductal adenocarcinoma adrenal cortex carcinoma breast cancer Duchenne muscular dystrophy exocrine pancreatic carcinoma hepatocellular carcinoma lung carcinoma non-small cell lung carcinoma pancreatic neoplasm psoriasis atypical teratoid rhabdoid tumor coronary artery disease gastric cancer malignant glioma medulloblastoma osteosarcoma pituitary cancer sinusitis bipolar disorder cystic fibrosis gastric carcinoma lung cancer

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.