3DKU

Crystal structure of Nudix hydrolase Orf153, ymfB, from Escherichia coli K-1

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	d3dkua_	Alpha and beta proteins (a+b)	Nudix	Nudix	automated matches	automated matches	(Escherichia coli APEC O1 ) [TaxId: 405955 ],	SCOPe (2.08)
B	d3dkub_	Alpha and beta proteins (a+b)	Nudix	Nudix	automated matches	automated matches	(Escherichia coli APEC O1 ) [TaxId: 405955 ],	SCOPe (2.08)
C	d3dkuc_	Alpha and beta proteins (a+b)	Nudix	Nudix	automated matches	automated matches	(Escherichia coli APEC O1 ) [TaxId: 405955 ],	SCOPe (2.08)
D	d3dkud_	Alpha and beta proteins (a+b)	Nudix	Nudix	automated matches	automated matches	(Escherichia coli APEC O1 ) [TaxId: 405955 ],	SCOPe (2.08)
E	d3dkue_	Alpha and beta proteins (a+b)	Nudix	Nudix	automated matches	automated matches	(Escherichia coli APEC O1 ) [TaxId: 405955 ],	SCOPe (2.08)
F	d3dkuf_	Alpha and beta proteins (a+b)	Nudix	Nudix	automated matches	automated matches	(Escherichia coli APEC O1 ) [TaxId: 405955 ],	SCOPe (2.08)
G	d3dkug_	Alpha and beta proteins (a+b)	Nudix	Nudix	automated matches	automated matches	(Escherichia coli APEC O1 ) [TaxId: 405955 ],	SCOPe (2.08)
H	d3dkuh_	Alpha and beta proteins (a+b)	Nudix	Nudix	automated matches	automated matches	(Escherichia coli APEC O1 ) [TaxId: 405955 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Nudix	8081766	3000098	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nudix	8081766	3000098	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nudix	8081766	3000098	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Nudix	8081766	3000098	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Nudix	8081766	3000098	SCOP2B (2022-06-29)
F	SCOP2 Family	MutT-like	8081765	4001887	SCOP2 (2022-06-29)
F	SCOP2 Superfamily	Nudix	8081766	3000098	SCOP2 (2022-06-29)
G	SCOP2B Superfamily	Nudix	8081766	3000098	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Nudix	8081766	3000098	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	PF00293	e3dkuA1	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: PF00293	ECOD (1.6)
B	PF00293	e3dkuB1	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: PF00293	ECOD (1.6)
C	PF00293	e3dkuC1	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: PF00293	ECOD (1.6)
D	PF00293	e3dkuD1	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: PF00293	ECOD (1.6)
E	PF00293	e3dkuE1	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: PF00293	ECOD (1.6)
F	PF00293	e3dkuF1	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: PF00293	ECOD (1.6)
G	PF00293	e3dkuG1	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: PF00293	ECOD (1.6)
H	PF00293	e3dkuH1	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: PF00293	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)
B	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (4.3.0)
C	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (4.3.0)
D	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (4.3.0)
E	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (4.3.0)
F	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (4.3.0)
G	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (4.3.0)
H	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	PF00293	NUDIX domain (NUDIX)	NUDIX domain	-	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, H	Putative phosphohydrolase	pyrophosphatase activity nucleoside diphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity ribonucleoside triphosphate phosphatase activity thiamine diphosphate phosphatase activity	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR000086	NUDIX hydrolase domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR015797	NUDIX hydrolase-like domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR020084	NUDIX hydrolase, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H	IPR020476	NUDIX hydrolase	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR033713	Phosphatase NudJ	Family

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.