5BKE | pdb_00005bke

Crystal structure of AAD-2 in complex with Mn(II) and N-oxalylglycine

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	d5bkea_	All beta proteins	Double-stranded beta-helix	Clavaminate synthase-like	automated matches	automated matches	(Bradyrhizobium diazoefficiens USDA 110 ) [TaxId: 224911 ],	SCOPe (2.08)
B	d5bkeb_	All beta proteins	Double-stranded beta-helix	Clavaminate synthase-like	automated matches	automated matches	(Bradyrhizobium diazoefficiens USDA 110 ) [TaxId: 224911 ],	SCOPe (2.08)
C	d5bkec_	All beta proteins	Double-stranded beta-helix	Clavaminate synthase-like	automated matches	automated matches	(Bradyrhizobium diazoefficiens USDA 110 ) [TaxId: 224911 ],	SCOPe (2.08)
D	d5bked_	All beta proteins	Double-stranded beta-helix	Clavaminate synthase-like	automated matches	automated matches	(Bradyrhizobium diazoefficiens USDA 110 ) [TaxId: 224911 ],	SCOPe (2.08)
E	d5bkee_	All beta proteins	Double-stranded beta-helix	Clavaminate synthase-like	automated matches	automated matches	(Bradyrhizobium diazoefficiens USDA 110 ) [TaxId: 224911 ],	SCOPe (2.08)
F	d5bkef_	All beta proteins	Double-stranded beta-helix	Clavaminate synthase-like	automated matches	automated matches	(Bradyrhizobium diazoefficiens USDA 110 ) [TaxId: 224911 ],	SCOPe (2.08)
G	d5bkeg_	All beta proteins	Double-stranded beta-helix	Clavaminate synthase-like	automated matches	automated matches	(Bradyrhizobium diazoefficiens USDA 110 ) [TaxId: 224911 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Clavaminate synthase-like	8100088	3001848	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Clavaminate synthase-like	8100088	3001848	SCOP2B (2022-06-29)
C	SCOP2 Family	TauD/TfdA-like	8100087	4002161	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Clavaminate synthase-like	8100088	3001848	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	Clavaminate synthase-like	8100088	3001848	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Clavaminate synthase-like	8100088	3001848	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Clavaminate synthase-like	8100088	3001848	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Clavaminate synthase-like	8100088	3001848	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		e5bkeA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F:	ECOD (v294.1)
B	ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	e5bkeB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	ECOD (v294.1)
C	LRR_6	e5bkeC1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: RIFT-related	T: FMN-binding split barrel 2	F: LRR_6	ECOD (v294.1)
D	ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	e5bkeD1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	ECOD (v294.1)
E	ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	e5bkeE1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	ECOD (v294.1)
F	DAO	e5bkeF1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DAO	ECOD (v294.1)
G	ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	e5bkeG1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.60.130.10	Alpha Beta	4-Layer Sandwich	Double-stranded beta-helix	Clavaminate synthase-like	CATH (utative)
B	3.60.130.10	Alpha Beta	4-Layer Sandwich	Double-stranded beta-helix	Clavaminate synthase-like	CATH (utative)
C	3.60.130.10	Alpha Beta	4-Layer Sandwich	Double-stranded beta-helix	Clavaminate synthase-like	CATH (utative)
D	3.60.130.10	Alpha Beta	4-Layer Sandwich	Double-stranded beta-helix	Clavaminate synthase-like	CATH (utative)
E	3.60.130.10	Alpha Beta	4-Layer Sandwich	Double-stranded beta-helix	Clavaminate synthase-like	CATH (utative)
F	3.60.130.10	Alpha Beta	4-Layer Sandwich	Double-stranded beta-helix	Clavaminate synthase-like	CATH (utative)
G	3.60.130.10	Alpha Beta	4-Layer Sandwich	Double-stranded beta-helix	Clavaminate synthase-like	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G	PF02668	Taurine catabolism dioxygenase TauD, TfdA family (TauD)	Taurine catabolism dioxygenase TauD, TfdA family	This family consists of taurine catabolism dioxygenases of the TauD, TfdA family. TauD from E. coli Swiss:P37610 is a alpha-ketoglutarate-dependent taurine dioxygenase [1]. This enzyme catalyses the oxygenolytic release of sulfite from taurine [1]. ...	This family consists of taurine catabolism dioxygenases of the TauD, TfdA family. TauD from E. coli Swiss:P37610 is a alpha-ketoglutarate-dependent taurine dioxygenase [1]. This enzyme catalyses the oxygenolytic release of sulfite from taurine [1]. TfdA from Burkholderia sp. Swiss:Q45423 is a 2,4-dichlorophenoxyacetic acid/alpha-ketoglutarate dioxygenase [2]. TfdA from Alcaligenes eutrophus JMP134 Swiss:P10088 is a 2,4-dichlorophenoxyacetate monooxygenase [3]. Also included are gamma-Butyrobetaine hydroxylase enzymes EC:1.14.11.1 [4].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G	Alpha-ketoglutarate-dependent 2,4-dichlorophenoxyacetate dioxygenase	oxidoreductase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen 2-oxoglutarate-dependent dioxygenase activity catalytic activity dioxygenase activity cation binding ion binding binding metal ion binding small molecule binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G	IPR003819	TauD/TfdA-like domain	Domain
A, B, C, D, E A, B, C, D, E, F, G	IPR051178	TfdA dioxygenase	Family
A, B, C, D, E A, B, C, D, E, F, G	IPR042098	Glutarate 2-hydroxylase 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.