1JNU

Photoexcited structure of the plant photoreceptor domain, phy3 LOV2

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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1jnua_	Alpha and beta proteins (a+b)	Profilin-like	PYP-like sensor domain (PAS domain)	Flavin-binding PAS domain	Photoreceptor phy3 flavin-binding domain, lov2	(Adiantum capillus-veneris ) [TaxId: 13818 ],	SCOPe (2.08)
B	d1jnub_	Alpha and beta proteins (a+b)	Profilin-like	PYP-like sensor domain (PAS domain)	Flavin-binding PAS domain	Photoreceptor phy3 flavin-binding domain, lov2	(Adiantum capillus-veneris ) [TaxId: 13818 ],	SCOPe (2.08)
C	d1jnuc_	Alpha and beta proteins (a+b)	Profilin-like	PYP-like sensor domain (PAS domain)	Flavin-binding PAS domain	Photoreceptor phy3 flavin-binding domain, lov2	(Adiantum capillus-veneris ) [TaxId: 13818 ],	SCOPe (2.08)
D	d1jnud_	Alpha and beta proteins (a+b)	Profilin-like	PYP-like sensor domain (PAS domain)	Flavin-binding PAS domain	Photoreceptor phy3 flavin-binding domain, lov2	(Adiantum capillus-veneris ) [TaxId: 13818 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Flavin-binding PAS domain	8027579	4003660	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PYP-like sensor domain (PAS domain)	8039958	3000471	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	PYP-like sensor domain (PAS domain)	8039958	3000471	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PYP-like sensor domain (PAS domain)	8039958	3000471	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	PYP-like sensor domain (PAS domain)	8039958	3000471	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	PAS	e1jnuA1	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: PAS	ECOD (1.6)
B	PAS	e1jnuB1	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: PAS	ECOD (1.6)
C	PAS	e1jnuC1	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: PAS	ECOD (1.6)
D	PAS	e1jnuD1	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: PAS	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.450.20	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	PAS domain	CATH (4.3.0)
B	3.30.450.20	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	PAS domain	CATH (4.3.0)
C	3.30.450.20	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	PAS domain	CATH (4.3.0)
D	3.30.450.20	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	PAS domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF13426	PAS domain (PAS_9)	PAS domain	This domain is found in many signalling proteins in which it functions as a sensor domain. It recognises FMN, Zn(II), FAD and riboflavin (MAtilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	PHY3 PROTEIN	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups blue light photoreceptor activity molecular transducer activity photoreceptor activity signaling receptor activity	regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process regulation of nitrogen compound metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process organic substance metabolic process heterocycle metabolic process organic substance biosynthetic process nitrogen compound metabolic process regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process regulation of nitrogen compound metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process organic substance metabolic process heterocycle metabolic process organic substance biosynthetic process nitrogen compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process cellular metabolic process biological regulation cellular nitrogen compound metabolic process primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process heterocycle biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process aromatic compound biosynthetic process organic cyclic compound biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process cellular aromatic compound metabolic process phosphorylation phosphate-containing compound metabolic process phosphorus metabolic process detection of light stimulus response to light stimulus detection of external stimulus detection of stimulus response to stimulus detection of visible light response to external stimulus response to abiotic stimulus response to radiation detection of abiotic stimulus	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR017441	Protein kinase, ATP binding site	Binding Site
A, B, C, D	IPR013515	Phytochrome, central region	Domain
A, B, C, D	IPR000014	PAS domain	Domain
A, B, C, D	IPR043150	Phytochrome, PHY domain superfamily	Homologous Superfamily
A, B, C, D	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR013654	PAS fold-2	Domain
A, B, C, D	IPR035965	PAS domain superfamily	Homologous Superfamily
A, B, C, D	IPR001610	PAC motif	Repeat
A, B, C, D	IPR000700	PAS-associated, C-terminal	Domain
A, B, C, D	IPR013516	Phytochrome chromophore binding site	Binding Site
A, B, C, D	IPR000719	Protein kinase domain	Domain
A, B, C, D	IPR003018	GAF domain	Domain
A, B, C, D	IPR029016	GAF-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR001294	Phytochrome	Family
A, B, C, D	IPR008271	Serine/threonine-protein kinase, active site	Active Site
A, B, C, D	IPR016132	Phytochrome chromophore attachment domain	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.