1YDY | pdb_00001ydy

Crystal structure of periplasmic glycerophosphodiester phosphodiesterase from Escherichia coli

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	d1ydya_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	PLC-like phosphodiesterases	Glycerophosphoryl diester phosphodiesterase	Glycerophosphodiester phosphodiesterase GlpQ	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1ydyb_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	PLC-like phosphodiesterases	Glycerophosphoryl diester phosphodiesterase	Glycerophosphodiester phosphodiesterase GlpQ	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Glycerophosphoryl diester phosphodiesterase	8021934	4000418	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PLC-like phosphodiesterases	8034314	3000615	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	PLC-like phosphodiesterases	8034314	3000615	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	GDPD	e1ydyA1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: GDPD	ECOD (1.6)
B	GDPD	e1ydyB1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: GDPD	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.20.20.190	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphatidylinositol (PI) phosphodiesterase	CATH (4.3.0)
B	3.20.20.190	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphatidylinositol (PI) phosphodiesterase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF03009	Glycerophosphoryl diester phosphodiesterase family (GDPD)	Glycerophosphoryl diester phosphodiesterase family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Glycerophosphoryl diester phosphodiesterase	phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds phosphoric diester hydrolase activity glycerophosphodiester phosphodiesterase activity hydrolase activity catalytic activity cation binding ion binding binding calcium ion binding metal ion binding small molecule binding	carbohydrate metabolic process polyol metabolic process primary metabolic process metabolic process cellular process alcohol metabolic process small molecule metabolic process glycerol metabolic process lipid catabolic process catabolic process phospholipid catabolic process glycerophospholipid metabolic process glycerolipid catabolic process organophosphate catabolic process carbohydrate metabolic process polyol metabolic process primary metabolic process metabolic process cellular process alcohol metabolic process small molecule metabolic process glycerol metabolic process lipid catabolic process catabolic process phospholipid catabolic process glycerophospholipid metabolic process glycerolipid catabolic process organophosphate catabolic process phospholipid metabolic process organophosphate metabolic process phosphate-containing compound metabolic process glycerophospholipid catabolic process glycerolipid metabolic process phosphorus metabolic process lipid metabolic process	cellular anatomical structure periplasmic space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR030395	Glycerophosphodiester phosphodiesterase domain	Domain
A, B	IPR017946	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain 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.