1H9U

The structure of the human retinoid-X-receptor beta ligand binding domain in complex with the specific synthetic agonist LG100268

External Resource: Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1h9ua_	All alpha proteins	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	Retinoid-X receptor beta (RXR-beta)	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1h9ub_	All alpha proteins	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	Retinoid-X receptor beta (RXR-beta)	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1h9uc_	All alpha proteins	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	Retinoid-X receptor beta (RXR-beta)	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d1h9ud_	All alpha proteins	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	Retinoid-X receptor beta (RXR-beta)	(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	SCOP2 Family	Nuclear receptor ligand-binding domain	8027067	4001384	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nuclear receptor ligand-binding domain	8039446	3001442	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8039446	3001442	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8039446	3001442	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8039446	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	PF00104	e1h9uA2	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: PF00104	ECOD (1.6)
B	PF00104	e1h9uB2	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: PF00104	ECOD (1.6)
C	PF00104	e1h9uC2	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: PF00104	ECOD (1.6)
D	PF00104	e1h9uD2	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: PF00104	ECOD (1.6)

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)
B	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)
D	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, B, C, D	RETINOID X RECEPTOR, BETA	DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding retinoic acid-responsive element 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 transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding nuclear steroid receptor activity DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding retinoic acid-responsive element 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 transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding nuclear steroid 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 nuclear receptor activity ligand-activated 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	developmental process cellular developmental process cell differentiation cellular process cellular response to stimulus regulation of biological process response to organic substance regulation of cellular process response to stimulus signaling response to endogenous stimulus biological regulation hormone-mediated signaling pathway cell communication developmental process cellular developmental process cell differentiation cellular process cellular response to stimulus regulation of biological process response to organic substance regulation of cellular process response to stimulus signaling response to endogenous stimulus biological regulation hormone-mediated signaling pathway cell communication cellular response to endogenous stimulus cellular response to chemical stimulus response to hormone response to chemical signal transduction cellular response to organic substance cellular response to hormone stimulus multicellular organismal process regulation of developmental process positive regulation of biological process regulation of biomineral tissue development regulation of bone mineralization positive regulation of ossification positive regulation of developmental process multicellular organism development positive regulation of biomineral tissue development ossification anatomical structure development biomineral tissue development regulation of multicellular organismal process regulation of multicellular organismal development bone mineralization animal organ development tissue development positive regulation of bone mineralization positive regulation of multicellular organismal process regulation of ossification intracellular receptor signaling pathway retinoic acid receptor signaling pathway response to retinoic acid response to lipid response to oxygen-containing compound regulation of vitamin D receptor signaling pathway positive regulation of cell communication response to nutrient levels regulation of response to nutrient levels positive regulation of signal transduction regulation of signal transduction response to vitamin cellular response to vitamin D positive regulation of response to stimulus response to vitamin D response to organic cyclic compound positive regulation of cellular process regulation of signaling response to nutrient cellular response to organic cyclic compound cellular response to oxygen-containing compound vitamin D receptor signaling pathway cellular response to nutrient levels cellular response to vitamin regulation of response to stimulus cellular response to lipid positive regulation of vitamin D receptor signaling pathway regulation of cell communication cellular response to nutrient positive regulation of signaling mRNA transcription by RNA polymerase II cellular biosynthetic process RNA metabolic process mRNA transcription nucleobase-containing compound metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process organic substance metabolic process transcription by RNA polymerase II organic substance biosynthetic process cellular metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process organic cyclic compound metabolic process biosynthetic process organic cyclic compound biosynthetic process metabolic process macromolecule metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of metabolic process regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of nucleobase-containing compound metabolic process regulation of cellular metabolic process positive regulation of RNA metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of DNA-templated transcription positive regulation of cellular metabolic process positive regulation of biosynthetic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of macromolecule metabolic process regulation of cellular biosynthetic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle RNA polymerase II transcription regulator complex protein-containing complex nuclear protein-containing complex transcription regulator complex cytoplasm cytosol nucleoplasm protein-DNA complex chromatin chromosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR000003	Retinoid X receptor/HNF4	Family
A, B, C, D	IPR001628	Zinc finger, nuclear hormone receptor-type	Domain
A, B, C, D	IPR001723	Nuclear hormone receptor	Family
A, B, C, D	IPR013088	Zinc finger, NHR/GATA-type	Homologous Superfamily
A, B, C, D	IPR000536	Nuclear hormone receptor, ligand-binding domain	Domain
A, B, C, D	IPR035500	Nuclear hormone receptor-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: P28702	breast carcinoma primary cutaneous T-cell lymphoma triple-negative breast carcinoma astrocytic tumor cervical cancer gastric cancer hereditary diffuse gastric adenocarcinoma malignant ependymoma Mammary Neoplasms oligodendroglioma Sjogren syndrome breast cancer gastric neoplasm IgA glomerulonephritis osteosarcoma breast carcinoma primary cutaneous T-cell lymphoma triple-negative breast carcinoma astrocytic tumor cervical cancer gastric cancer hereditary diffuse gastric adenocarcinoma malignant ependymoma Mammary Neoplasms oligodendroglioma Sjogren syndrome breast cancer gastric neoplasm IgA glomerulonephritis osteosarcoma subependymal giant cell astrocytoma Hashimoto thyroiditis medulloblastoma

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 R01GM133198.