6EU9 | pdb_00006eu9

Crystal structure of Platynereis dumerilii RAR ligand-binding domain in complex with all-trans retinoic acid

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d6eu9a_	All alpha proteins	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	automated matches	automated matches	(Platynereis dumerilii ) [TaxId: 6359 ],	SCOPe (2.08)
B	d6eu9b_	All alpha proteins	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	automated matches	automated matches	(Platynereis dumerilii ) [TaxId: 6359 ],	SCOPe (2.08)
C	d6eu9c_	All alpha proteins	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	automated matches	automated matches	(Platynereis dumerilii ) [TaxId: 6359 ],	SCOPe (2.08)
D	d6eu9d_	All alpha proteins	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	automated matches	automated matches	(Platynereis dumerilii ) [TaxId: 6359 ],	SCOPe (2.08)

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	8095137	3001442	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8095137	3001442	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8095137	3001442	SCOP2B (2022-06-29)
D	SCOP2 Family	Nuclear receptor ligand-binding domain	8095136	4001384	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	Nuclear receptor ligand-binding domain	8095137	3001442	SCOP2 (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_1	e6eu9A1	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_1	ECOD (1.6)
B	Hormone_recep_1	e6eu9B1	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_1	ECOD (1.6)
C	Hormone_recep_1	e6eu9C1	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_1	ECOD (1.6)
D	Hormone_recep_1	e6eu9D1	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_1	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)

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	Retinoic acid 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 transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding 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 transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding protein binding nuclear glucocorticoid receptor binding DNA-binding transcription factor binding nuclear 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 ligand-modulated transcription factor activity	cellular response to stimulus cellular response to nitrogen compound response to corticotropin-releasing hormone response to stimulus 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 cellular response to chemical stimulus response to hormone response to chemical cellular response to stimulus cellular response to nitrogen compound response to corticotropin-releasing hormone response to stimulus 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 cellular response to chemical stimulus response to hormone response to chemical cellular process cellular response to corticotropin-releasing hormone stimulus cellular response to hormone stimulus regulation of biological process regulation of cellular process intracellular receptor signaling pathway signaling biological regulation retinoic acid receptor signaling pathway hormone-mediated signaling pathway intracellular signal transduction cell communication signal transduction nuclear receptor-mediated signaling pathway	protein-containing complex transcription regulator complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR001723	Nuclear hormone receptor	Family
A, B, C, D	IPR003078	Retinoic acid 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

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.