3A40

Crystal structure of the human VDR ligand binding domain bound to the synthetic agonist compound 2alpha-methyl-AMCR277B(C23R)

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 X]	d3a40x_	All alpha proteins	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	automated matches	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 X]	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8033916	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 X]	Hormone_recep	e3a40X1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth X]	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 X]	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 X]	Vitamin D3 receptor	vitamin binding calcitriol binding binding D3 vitamins binding organic cyclic compound binding vitamin D binding steroid binding lipid binding small molecule binding DNA binding nucleic acid binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity vitamin binding calcitriol binding binding D3 vitamins binding organic cyclic compound binding vitamin D binding steroid binding lipid binding small molecule binding DNA binding nucleic acid binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity lithocholic acid binding organic acid binding bile acid binding ion binding anion binding carboxylic acid binding monocarboxylic acid binding nuclear receptor activity molecular transducer activity ligand-activated transcription factor activity signaling receptor activity 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 transcription factor binding nuclear retinoic acid receptor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding protein binding nuclear retinoid X receptor binding DNA-binding transcription factor binding cation binding transition metal ion binding zinc ion binding metal ion binding bile acid nuclear receptor activity	developmental process multicellular organism development multicellular organismal process skeletal system development anatomical structure development system development regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process developmental process multicellular organism development multicellular organismal process skeletal system development anatomical structure development system development regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological 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 system process digestion intestinal absorption digestive system process inorganic ion homeostasis intracellular calcium ion homeostasis homeostatic process calcium ion homeostasis cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis 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 animal organ development tissue development positive regulation of bone mineralization positive regulation of multicellular organismal process regulation of ossification 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 vitamin D 24-hydroxylase activity regulation of catalytic activity positive regulation of catalytic activity regulation of oxidoreductase activity positive regulation of oxidoreductase activity regulation of molecular function positive regulation of molecular function regulation of monooxygenase activity positive regulation of monooxygenase activity regulation of vitamin D 24-hydroxylase activity response to bile acid response to lipid response to oxygen-containing compound response to organic cyclic compound anatomical structure morphogenesis cell morphogenesis mRNA transcription by RNA polymerase II RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process mRNA transcription mRNA metabolic 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 regulation of body fluid levels secretion transport mammary gland development gland development establishment of localization body fluid secretion localization lactation regulation of biological quality negative regulation of cell population proliferation cell population proliferation regulation of keratinocyte proliferation negative regulation of biological process negative regulation of keratinocyte proliferation regulation of cell population proliferation negative regulation of cellular process regulation of epithelial cell proliferation epithelial cell proliferation negative regulation of epithelial cell proliferation keratinocyte proliferation regulation of primary metabolic process negative regulation of RNA biosynthetic process regulation of RNA metabolic 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 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 regulation of DNA-templated transcription negative regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process transmembrane transport phosphate ion transmembrane transport phosphate ion transport inorganic ion transmembrane transport inorganic anion transmembrane transport inorganic anion transport apoptotic process involved in morphogenesis mammary gland morphogenesis apoptotic process involved in mammary gland involution cell death apoptotic process involved in development gland morphogenesis tissue remodeling mammary gland involution animal organ morphogenesis apoptotic process programmed cell death cellular developmental process cell differentiation regulation of calcidiol 1-monooxygenase activity response to nutrient levels response to vitamin cellular response to vitamin D response to vitamin D 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 cellular response to lipid cellular response to nutrient branching involved in mammary gland duct morphogenesis multi-multicellular organism process reproductive process maternal process involved in female pregnancy branching morphogenesis of an epithelial tube developmental process involved in reproduction tube morphogenesis mammary gland branching involved in pregnancy epithelial tube morphogenesis female pregnancy epithelium development tube development multicellular organismal reproductive process morphogenesis of an epithelium mammary gland duct morphogenesis tissue morphogenesis mammary gland epithelium development morphogenesis of a branching structure multi-organism reproductive process morphogenesis of a branching epithelium positive regulation of cell communication regulation of response to nutrient levels positive regulation of signal transduction regulation of signal transduction positive regulation of intracellular signal transduction regulation of response to stimulus regulation of vitamin D receptor signaling pathway positive regulation of response to stimulus regulation of intracellular signal transduction regulation of signaling positive regulation of vitamin D receptor signaling pathway regulation of cell communication positive regulation of signaling placenta development maternal placenta development decidualization monoatomic ion transport monoatomic cation transport calcium ion transport metal ion transport positive regulation of keratinocyte differentiation regulation of epidermal cell differentiation epidermis development regulation of cell differentiation epithelial cell differentiation regulation of epithelial cell differentiation positive regulation of cell differentiation epidermal cell differentiation positive regulation of epidermis development positive regulation of epithelial cell differentiation skin development keratinocyte differentiation regulation of epidermis development regulation of keratinocyte differentiation positive regulation of epidermal cell differentiation bile acid signaling pathway nuclear receptor-mediated bile acid signaling pathway regulation of programmed cell death positive regulation of apoptotic process involved in mammary gland involution positive regulation of apoptotic process involved in morphogenesis positive regulation of programmed cell death positive regulation of apoptotic process involved in development regulation of apoptotic process regulation of apoptotic process involved in development positive regulation of apoptotic process regulation of apoptotic process involved in morphogenesis	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome protein-containing complex receptor complex RNA polymerase II transcription regulator complex membrane-bounded organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome protein-containing complex receptor complex RNA polymerase II transcription regulator complex membrane-bounded organelle nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth X]	IPR001628	Zinc finger, nuclear hormone receptor-type	Domain
A [auth X]	IPR013088	Zinc finger, NHR/GATA-type	Homologous Superfamily
A [auth X]	IPR042153	VDR, DNA-binding domain	Domain
A [auth X]	IPR050234	Nuclear hormone receptor family NR1 subfamily	Family
A [auth X]	IPR001723	Nuclear hormone receptor	Family
A [auth X]	IPR000324	Vitamin D receptor	Family
A [auth X]	IPR000536	Nuclear hormone receptor, ligand-binding domain	Domain
A [auth X]	IPR035500	Nuclear hormone receptor-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth X]	Pharos: P11473	rickets vitamin D-dependent rickets, type 2A Vitamin D Deficiency transitional cell carcinoma osteoporosis B-cell chronic lymphocytic leukemia temporal lobe epilepsy hyperparathyroidism hypertensive disorder Mendelian disease alopecia lead poisoning cancer multiple sclerosis uremia rickets vitamin D-dependent rickets, type 2A Vitamin D Deficiency transitional cell carcinoma osteoporosis B-cell chronic lymphocytic leukemia temporal lobe epilepsy hyperparathyroidism hypertensive disorder Mendelian disease alopecia lead poisoning cancer multiple sclerosis uremia prostate cancer breast carcinoma cerebral infarction nephrolithiasis ulcerative colitis osteomalacia vitamin D-dependent rickets, type 2 pancreatic ductal adenocarcinoma adenoma inflammatory bowel disease postmenopausal osteoporosis asthma invasive ductal breast carcinoma prostate carcinoma bipolar disorder lung adenocarcinoma renal osteodystrophy breast fibroadenoma malignant ependymoma schizophrenia malignant pancreatic neoplasm skin basal cell carcinoma ductal breast carcinoma in situ nephrosclerosis osteosarcoma pancreatic intraductal papillary-mucinous neoplasm X-linked dominant hypophosphatemic rickets hypoparathyroidism androgenetic alopecia intellectual disability breast cancer lung cancer malignant mesothelioma sclerosing cholangitis tuberculosis osteogenesis imperfecta ovarian cancer pituitary cancer alopecia areata hypophosphatemia intervertebral disc degenerative disorder benign neoplasm leprosy 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.