3O52 | pdb_00003o52

Structure of the E.coli GDP-mannose hydrolase (yffh) in complex with tartrate

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)
E	d3o52e_	Alpha and beta proteins (a+b)	Nudix	Nudix	MutT-like	ADP-ribose pyrophosphatase homologue YffH	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
D	d3o52d_	Alpha and beta proteins (a+b)	Nudix	Nudix	MutT-like	ADP-ribose pyrophosphatase homologue YffH	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C	d3o52c_	Alpha and beta proteins (a+b)	Nudix	Nudix	MutT-like	ADP-ribose pyrophosphatase homologue YffH	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d3o52b_	Alpha and beta proteins (a+b)	Nudix	Nudix	MutT-like	ADP-ribose pyrophosphatase homologue YffH	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d3o52a_	Alpha and beta proteins (a+b)	Nudix	Nudix	MutT-like	ADP-ribose pyrophosphatase homologue YffH	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E	SCOP2B Superfamily	Nudix	8035905	3000098	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Nudix	8035905	3000098	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nudix	8035905	3000098	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nudix	8035905	3000098	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nudix	8035905	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)
E	Radical_SAM	e3o52E1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Radical_SAM	ECOD (v294.1)
D	Radical_SAM	e3o52D1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Radical_SAM	ECOD (v294.1)
C	Radical_SAM	e3o52C1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Radical_SAM	ECOD (v294.1)
B	Radical_SAM	e3o52B1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Radical_SAM	ECOD (v294.1)
A	Cupin_2	e3o52A1	A: a/b three-layered sandwiches	X: EF-hand	H: Insect pheromone/odorant-binding proteins	T: Insect pheromone/odorant-binding proteins	F: Cupin_2	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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	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	GDP-mannose pyrophosphatase nudK	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding GDP-mannose hydrolase activity pyrophosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity identical protein binding protein binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding GDP-mannose hydrolase activity pyrophosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity identical protein binding protein binding protein homodimerization activity protein dimerization activity	ribose phosphate metabolic process organophosphate metabolic process phosphate-containing compound metabolic process carbohydrate derivative metabolic process metabolic process cellular process phosphorus metabolic process nucleoside phosphate metabolic process nucleobase-containing compound metabolic process nucleobase-containing small molecule metabolic process small molecule metabolic process primary metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E	IPR000086	NUDIX hydrolase domain	Domain
A, B, C, D, E	IPR015797	NUDIX hydrolase-like domain superfamily	Homologous Superfamily
A, B, C, D, E	IPR004385	Nucleoside diphosphate pyrophosphatase	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.