3DKU | pdb_00003dku

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)
H	d3dkuh_	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)
F	d3dkuf_	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)
D	d3dkud_	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)
B	d3dkub_	Alpha and beta proteins (a+b)	Nudix	Nudix	automated matches	automated matches	(Escherichia coli APEC O1 ) [TaxId: 405955 ],	SCOPe (2.08)
A	d3dkua_	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)
H	SCOP2B Superfamily	Nudix	8081766	3000098	SCOP2B (2022-06-29)
G	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)
E	SCOP2B Superfamily	Nudix	8081766	3000098	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Nudix	8081766	3000098	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nudix	8081766	3000098	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nudix	8081766	3000098	SCOP2B (2022-06-29)
A	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)
H	NUDIX	e3dkuH1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: NUDIX	ECOD (v294.1)
G	NUDIX	e3dkuG1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: NUDIX	ECOD (v294.1)
F	NUDIX	e3dkuF1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: NUDIX	ECOD (v294.1)
E	NUDIX	e3dkuE1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: NUDIX	ECOD (v294.1)
D	NUDIX	e3dkuD1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: NUDIX	ECOD (v294.1)
C	NUDIX	e3dkuC1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: NUDIX	ECOD (v294.1)
B	NUDIX	e3dkuB1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: NUDIX	ECOD (v294.1)
A	ubiquitin	e3dkuA1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: FAD-dependent thiol oxidase	T: FAD-dependent thiol oxidase	F: ubiquitin	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	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)
F	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)
D	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)
B	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (4.3.0)
A	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 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.