5BS6

Apo structure of transcriptional factor AraR from Bacteroides thetaiotaomicron VPI

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	d5bs6a2	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Nudix-associated domain	Hypothetical protein BT0354, C-terminal domain	(Bacteroides thetaiotaomicron VPI-5482 ) [TaxId: 226186 ],	SCOPe (2.08)
A	d5bs6a1	Alpha and beta proteins (a+b)	Nudix	Nudix	BT0354 N-terminal domain-like	Hypothetical protein BT0354, N-terminal domain	(Bacteroides thetaiotaomicron VPI-5482 ) [TaxId: 226186 ],	SCOPe (2.08)
B	d5bs6b2	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Nudix-associated domain	Hypothetical protein BT0354, C-terminal domain	(Bacteroides thetaiotaomicron VPI-5482 ) [TaxId: 226186 ],	SCOPe (2.08)
B	d5bs6b1	Alpha and beta proteins (a+b)	Nudix	Nudix	BT0354 N-terminal domain-like	Hypothetical protein BT0354, N-terminal domain	(Bacteroides thetaiotaomicron VPI-5482 ) [TaxId: 226186 ],	SCOPe (2.08)
B	d5bs6b3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Bacteroides thetaiotaomicron VPI-5482 ) [TaxId: 226186 ],	SCOPe (2.08)
C	d5bs6c2	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Nudix-associated domain	Hypothetical protein BT0354, C-terminal domain	(Bacteroides thetaiotaomicron VPI-5482 ) [TaxId: 226186 ],	SCOPe (2.08)
C	d5bs6c1	Alpha and beta proteins (a+b)	Nudix	Nudix	BT0354 N-terminal domain-like	Hypothetical protein BT0354, N-terminal domain	(Bacteroides thetaiotaomicron VPI-5482 ) [TaxId: 226186 ],	SCOPe (2.08)
C	d5bs6c3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Bacteroides thetaiotaomicron VPI-5482 ) [TaxId: 226186 ],	SCOPe (2.08)
D	d5bs6d2	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Nudix-associated domain	Hypothetical protein BT0354, C-terminal domain	(Bacteroides thetaiotaomicron VPI-5482 ) [TaxId: 226186 ],	SCOPe (2.08)
D	d5bs6d1	Alpha and beta proteins (a+b)	Nudix	Nudix	BT0354 N-terminal domain-like	Hypothetical protein BT0354, N-terminal domain	(Bacteroides thetaiotaomicron VPI-5482 ) [TaxId: 226186 ],	SCOPe (2.08)
D	d5bs6d3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Bacteroides thetaiotaomicron VPI-5482 ) [TaxId: 226186 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	BT0354-like	8003430	4000305	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nudix	8003431	3000098	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Winged helix DNA-binding domain	8003434	3000034	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Nudix	8003431	3000098	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Winged helix DNA-binding domain	8003434	3000034	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nudix	8003431	3000098	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Winged helix DNA-binding domain	8003434	3000034	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Nudix	8003431	3000098	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Winged helix DNA-binding domain	8003434	3000034	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	COG4111	e5bs6A2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: COG4111	ECOD (1.6)
A	NUDIX_1	e5bs6A1	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: NUDIX_1	ECOD (1.6)
B	COG4111	e5bs6B2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: COG4111	ECOD (1.6)
B	NUDIX_1	e5bs6B1	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: NUDIX_1	ECOD (1.6)
C	COG4111	e5bs6C2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: COG4111	ECOD (1.6)
C	NUDIX_1	e5bs6C1	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: NUDIX_1	ECOD (1.6)
D	COG4111	e5bs6D3	A: alpha arrays	X: HTH	H: HTH	T: winged	F: COG4111	ECOD (1.6)
D	NUDIX_1	e5bs6D2	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: NUDIX_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (4.3.0)
A	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
B	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (4.3.0)
B	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
C	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (4.3.0)
C	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
D	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (4.3.0)
D	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00293	NUDIX domain (NUDIX)	NUDIX domain	-	Domain
A, B, C, D	PF21906	NrtR DNA-binding winged helix domain (NrtR_WHD)	NrtR DNA-binding winged helix domain	This entry represents the C-terminal DNA-binding domain of bacterial transcriptional regulator NrtR which is involved in regulating the transcription of NAD biosynthetic genes. This domain has a winged helix-turn-helix structure [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	transcriptional regulator AraR	DNA binding binding organic cyclic compound binding nucleic acid binding hydrolase activity catalytic activity	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR000086	NUDIX hydrolase domain	Domain
A, B, C, D	IPR015797	NUDIX hydrolase-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR045830	AraR-like, winged helix DNA-binding domain	Domain
A, B, C, D	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR036390	Winged helix DNA-binding 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 R01GM133198.