5YD6 | pdb_00005yd6

Crystal structure of PG-bound Nurr1-LBD

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)
D	d5yd6d_	All alpha proteins	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	Orphan nuclear receptor NURR1	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d5yd6c_	All alpha proteins	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	Orphan nuclear receptor NURR1	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5yd6b_	All alpha proteins	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	Orphan nuclear receptor NURR1	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5yd6a_	All alpha proteins	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	Orphan nuclear receptor NURR1	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)
D	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8034384	3001442	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8034384	3001442	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8034384	3001442	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8034384	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)
D	LptF_LptG	e5yd6D1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: LptF_LptG	ECOD (v294.1)
C	p450	e5yd6C1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: p450	ECOD (v294.1)
B	LptF_LptG	e5yd6B1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: LptF_LptG	ECOD (v294.1)
A	LptF_LptG	e5yd6A1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: LptF_LptG	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.10.565.10	Mainly Alpha	Orthogonal Bundle	Retinoid X Receptor	Retinoid X Receptor	CATH (utative)
C	1.10.565.10	Mainly Alpha	Orthogonal Bundle	Retinoid X Receptor	Retinoid X Receptor	CATH (utative)
B	1.10.565.10	Mainly Alpha	Orthogonal Bundle	Retinoid X Receptor	Retinoid X Receptor	CATH (utative)
A	1.10.565.10	Mainly Alpha	Orthogonal Bundle	Retinoid X Receptor	Retinoid X Receptor	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	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, B, C, D	Nuclear receptor subfamily 4 group A member 2	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 nucleic acid binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity nuclear receptor activity molecular transducer activity 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 nucleic acid 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 sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific 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 nuclear retinoic acid receptor binding nuclear retinoid X receptor binding beta-catenin binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	developmental process multicellular organismal process head development forebrain development animal organ development brain development diencephalon development nervous system development multicellular organism development central nervous system development habenula development epithalamus development anatomical structure development system development developmental process multicellular organismal process head development forebrain development animal organ development brain development diencephalon development nervous system development multicellular organism development central nervous system development habenula development epithalamus development anatomical structure development system development cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling canonical Wnt signaling pathway biological regulation cell communication cellular process signal transduction Wnt signaling pathway regulation of amine metabolic process dopamine metabolic process primary metabolic process catechol-containing compound metabolic process regulation of primary metabolic process amine metabolic process catecholamine metabolic process phenol-containing compound metabolic process metabolic process regulation of catecholamine metabolic process regulation of metabolic process biogenic amine metabolic process regulation of dopamine metabolic process general adaptation syndrome response to stress multicellular organismal response to stress axonogenesis cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development central nervous system neuron development neuron projection development cell morphogenesis cellular component organization neurogenesis central nervous system neuron differentiation cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation cellular component organization or biogenesis central nervous system projection neuron axonogenesis central nervous system neuron axonogenesis plasma membrane bounded cell projection organization axon development cell morphogenesis involved in neuron differentiation generation of neurons anatomical structure morphogenesis neuron development RNA 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 biosynthetic process macromolecule metabolic process response to oxidative stress cellular response to chemical stimulus cellular response to stress response to chemical cellular response to oxidative stress cellular response to chemical stress biogenic amine biosynthetic process amine biosynthetic process dopamine biosynthetic process catecholamine biosynthetic process phenol-containing compound biosynthetic process catechol-containing compound biosynthetic process fat cell differentiation response to decreased oxygen levels response to hypoxia response to oxygen levels response to abiotic stimulus regulation of respiratory gaseous exchange regulation of multicellular organismal process respiratory gaseous exchange by respiratory system negative regulation of biological process negative regulation of RNA biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II 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 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 regulation of macromolecule metabolic process regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process 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 biological process 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 adult locomotory behavior behavior adult behavior locomotory behavior 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 oxygen-containing compound response to nitrogen compound cellular response to oxygen-containing compound cellular response to endogenous stimulus response to hormone cellular response to corticotropin-releasing hormone stimulus cellular response to hormone stimulus developmental maturation anatomical structure maturation neuron maturation cell maturation neuron apoptotic process negative regulation of neuron apoptotic process negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process apoptotic process programmed cell death regulation of neuron apoptotic process negative regulation of signaling regulation of signal transduction negative regulation of cell communication negative regulation of apoptotic signaling pathway regulation of signaling negative regulation of response to stimulus negative regulation of signal transduction apoptotic signaling pathway regulation of response to stimulus regulation of cell communication regulation of apoptotic signaling pathway dopaminergic neuron differentiation midbrain development midbrain dopaminergic neuron differentiation response to amine response to amphetamine neuron migration cell migration cell motility post-embryonic development	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body cellular anatomical structure nucleoplasm organelle lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body cellular anatomical structure nucleoplasm organelle lumen organelle membraneless organelle supramolecular complex nuclear ribonucleoprotein granule nuclear lumen protein-containing complex transcription regulator complex cytoplasm chromatin chromosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR003073	Nuclear receptor subfamily 4 group A member 2	Family
A, B, C, D	IPR001628	Zinc finger, nuclear hormone receptor-type	Domain
A, B, C, D	IPR013088	Zinc finger, NHR/GATA-type	Homologous Superfamily
A, B, C, D	IPR003070	Nuclear receptor subfamily 4 group A member 1-3	Family
A, B, C, D	IPR001723	Nuclear hormone receptor	Family
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: P43354	Parkinson disease psoriatic arthritis juvenile idiopathic arthritis Arsenic Poisoning bipolar disorder colorectal cancer rheumatoid arthritis exocrine pancreatic carcinoma skin disease glioblastoma ulcerative colitis interstitial lung disease acute myeloid leukemia late-onset Parkinson disease lymphoplasmacytic lymphoma Parkinson disease psoriatic arthritis juvenile idiopathic arthritis Arsenic Poisoning bipolar disorder colorectal cancer rheumatoid arthritis exocrine pancreatic carcinoma skin disease glioblastoma ulcerative colitis interstitial lung disease acute myeloid leukemia late-onset Parkinson disease lymphoplasmacytic lymphoma malignant glioma nasopharyngeal carcinoma B-cell chronic lymphocytic leukemia non-small cell lung carcinoma breast cancer colorectal carcinoma psoriasis endogenous depression schizophrenia gastric cancer transitional cell carcinoma hepatocellular carcinoma adrenal cortex carcinoma lung adenocarcinoma major depressive disorder malignant pancreatic neoplasm astrocytic tumor nephrosclerosis Barrett esophagus oligodendroglioma cocaine abuse pituitary cancer esophageal adenocarcinoma sinusitis gastric carcinoma tuberculosis interstitial cystitis large cell medulloblastoma lung cancer malignant ependymoma medulloblastoma atypical teratoid rhabdoid tumor osteosarcoma primitive neuroectodermal tumor

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.