5DEQ | pdb_00005deq

Crystal structure of transcriptional factor AraR from Bacteroides thetaiotaomicron VPI in complex with L-arabinose

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)
B	d5deqb2	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	d5deqb1	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)
A	d5deqa2	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	d5deqa1	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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Winged helix DNA-binding domain	8003434	3000034	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nudix	8003431	3000098	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nudix	8003431	3000098	SCOP2B (2022-06-29)
A	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)
B		e5deqB1	A: a/b three-layered sandwiches	X: C-terminal additional helical subdomain in reovirus polymerase lambda3	H: C-terminal additional helical subdomain in reovirus polymerase lambda3	T: C-terminal additional helical subdomain in reovirus polymerase lambda3	F:	ECOD (v294.1)
B	AARP2CN	e5deqB2	A: a/b three-layered sandwiches	X: Spectrin repeat-like	H: Spectrin repeat	T: Spectrin repeat	F: AARP2CN	ECOD (v294.1)
A		e5deqA1	A: a/b three-layered sandwiches	X: C-terminal additional helical subdomain in reovirus polymerase lambda3	H: C-terminal additional helical subdomain in reovirus polymerase lambda3	T: C-terminal additional helical subdomain in reovirus polymerase lambda3	F:	ECOD (v294.1)
A	AARP2CN	e5deqA2	A: a/b three-layered sandwiches	X: Spectrin repeat-like	H: Spectrin repeat	T: Spectrin repeat	F: AARP2CN	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00293	NUDIX domain (NUDIX)	NUDIX domain		Domain
A, B	PF21906	NrtR DNA-binding winged helix domain (WHD_NrtR)	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	TRANSCRIPTIONAL REGULATOR AraR	hydrolase activity catalytic activity	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR000086	NUDIX hydrolase domain	Domain
A, B	IPR015797	NUDIX hydrolase-like domain superfamily	Homologous Superfamily
A, B	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
A, B	IPR054105	NrtR, DNA-binding winged helix domain	Domain

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.