6W9M

Structure of the Ancestral Glucocorticoid Receptor 2 ligand binding domain in complex with vamorolone and SHP coregulator fragment

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
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	8094545	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	Hormone_recep	e6w9mA1	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	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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	Glucocorticoid Receptor	DNA binding sequence-specific DNA binding 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 organic cyclic compound binding estrogen response element binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding nuclear receptor activity DNA binding sequence-specific DNA binding 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 organic cyclic compound binding estrogen response element binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding nuclear receptor activity DNA-binding transcription factor activity, RNA polymerase II-specific molecular transducer activity transcription regulator activity ligand-activated transcription factor activity DNA-binding transcription factor activity signaling receptor activity	cellular response to stimulus regulation of cellular process intracellular receptor signaling pathway response to stimulus response to lipid signaling hormone-mediated signaling pathway intracellular signal transduction cell communication cellular response to endogenous stimulus response to hormone response to steroid hormone signal transduction nuclear receptor-mediated steroid hormone signaling pathway cellular response to stimulus regulation of cellular process intracellular receptor signaling pathway response to stimulus response to lipid signaling hormone-mediated signaling pathway intracellular signal transduction cell communication cellular response to endogenous stimulus response to hormone response to steroid hormone signal transduction nuclear receptor-mediated steroid hormone signaling pathway cellular response to steroid hormone stimulus response to organic cyclic compound steroid hormone receptor signaling pathway cellular response to hormone stimulus regulation of biological process response to endogenous stimulus biological regulation cellular response to organic cyclic compound cellular response to chemical stimulus response to chemical cellular response to lipid cellular process nuclear receptor-mediated signaling pathway	-
B	Nuclear receptor subfamily 0 group B member 2	protein binding binding protein domain specific binding molecular function inhibitor activity molecular function regulator activity transcription regulator inhibitor activity signaling receptor binding peroxisome proliferator activated receptor binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding nuclear thyroid hormone receptor binding DNA-binding transcription factor binding transcription corepressor activity protein binding binding protein domain specific binding molecular function inhibitor activity molecular function regulator activity transcription regulator inhibitor activity signaling receptor binding peroxisome proliferator activated receptor binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding nuclear thyroid hormone receptor binding DNA-binding transcription factor binding transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity identical protein binding protein homodimerization activity protein dimerization activity protein-containing complex binding nuclear retinoic acid receptor binding nuclear retinoid X receptor binding	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic 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 negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process rhythmic process circadian rhythm negative regulation of DNA-binding transcription factor activity negative regulation of molecular function regulation of molecular function regulation of DNA-binding transcription factor activity positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of gene expression positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process organic hydroxy compound metabolic process sterol metabolic process steroid metabolic process cholesterol metabolic process alcohol metabolic process secondary alcohol metabolic process small molecule metabolic process lipid metabolic process organic anion transport carboxylic acid transport transport lipid localization bile acid and bile salt transport lipid transport organic hydroxy compound transport establishment of localization organic acid transport localization monocarboxylic acid transport macromolecule localization response to hexose response to monosaccharide response to carbohydrate response to stimulus response to glucose response to chemical response to oxygen-containing compound circadian regulation of gene expression response to alcohol response to ethanol positive regulation of DNA-templated transcription positive regulation of nucleobase-containing compound metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process developmental process animal organ regeneration animal organ development anatomical structure development regeneration negative regulation of gene expression transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II protein localization positive regulation of cell communication regulation of localization establishment of protein localization nitrogen compound transport positive regulation of establishment of protein localization cell communication cellular macromolecule localization positive regulation of insulin secretion regulation of biological quality regulation of peptide hormone secretion regulation of hormone levels positive regulation of peptide hormone secretion establishment of protein localization to extracellular region protein secretion regulation of protein secretion regulation of secretion positive regulation of protein localization cellular localization regulation of hormone secretion regulation of protein localization regulation of peptide secretion signaling positive regulation of secretion by cell hormone secretion protein localization to extracellular region positive regulation of protein transport peptide secretion secretion by cell regulation of secretion by cell positive regulation of hormone secretion positive regulation of secretion amide transport signal release positive regulation of peptide secretion regulation of signaling secretion regulation of transport regulation of peptide transport regulation of establishment of protein localization cell-cell signaling export from cell regulation of protein transport positive regulation of protein secretion peptide transport positive regulation of transport protein transport regulation of cellular localization regulation of insulin secretion peptide hormone secretion hormone transport regulation of cell communication insulin secretion positive regulation of signaling cellular response to stimulus cell surface receptor signaling pathway Notch signaling pathway signal transduction response to organic cyclic compound	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle intracellular membrane-bounded organelle cytoplasm nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen membraneless organelle membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle intracellular membrane-bounded organelle cytoplasm nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen membraneless organelle intracellular membraneless organelle chromatin chromosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001723	Nuclear hormone receptor	Family
A	IPR000536	Nuclear hormone receptor, ligand-binding domain	Domain
A	IPR035500	Nuclear hormone receptor-like domain superfamily	Homologous Superfamily
A	IPR050200	Nuclear hormone receptor family NR3 subfamily	Family
B	IPR001723	Nuclear hormone receptor	Family
B	IPR000536	Nuclear hormone receptor, ligand-binding domain	Domain
B	IPR035500	Nuclear hormone receptor-like domain superfamily	Homologous Superfamily
B	IPR033544	Nuclear receptor subfamily 0 group B member 1/2	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: Q15466	obesity disorder Liver Cirrhosis, Experimental monogenic obesity acquired metabolic disease fatty liver disease lysosomal lipid storage disorder cholestasis drug-induced liver injury hepatocellular carcinoma malignant pancreatic neoplasm lung carcinoma

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.