1ZCC | pdb_00001zcc

Crystal structure of glycerophosphodiester phosphodiesterase from Agrobacterium tumefaciens str.C58

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)
F	d1zccf_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	PLC-like phosphodiesterases	Glycerophosphoryl diester phosphodiesterase	automated matches	(Agrobacterium fabrum str. C58 ) [TaxId: 176299 ],	SCOPe (2.08)
E	d1zcce_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	PLC-like phosphodiesterases	Glycerophosphoryl diester phosphodiesterase	automated matches	(Agrobacterium fabrum str. C58 ) [TaxId: 176299 ],	SCOPe (2.08)
D	d1zccd_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	PLC-like phosphodiesterases	Glycerophosphoryl diester phosphodiesterase	automated matches	(Agrobacterium fabrum str. C58 ) [TaxId: 176299 ],	SCOPe (2.08)
C	d1zccc_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	PLC-like phosphodiesterases	Glycerophosphoryl diester phosphodiesterase	automated matches	(Agrobacterium fabrum str. C58 ) [TaxId: 176299 ],	SCOPe (2.08)
B	d1zccb_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	PLC-like phosphodiesterases	Glycerophosphoryl diester phosphodiesterase	automated matches	(Agrobacterium fabrum str. C58 ) [TaxId: 176299 ],	SCOPe (2.08)
A	d1zcca1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	PLC-like phosphodiesterases	Glycerophosphoryl diester phosphodiesterase	Glycerophosphodiester phosphodiesterase UgpQ	(Agrobacterium fabrum str. C58 ) [TaxId: 176299 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	PLC-like phosphodiesterases	8035572	3000615	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	PLC-like phosphodiesterases	8035572	3000615	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	PLC-like phosphodiesterases	8035572	3000615	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PLC-like phosphodiesterases	8035572	3000615	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PLC-like phosphodiesterases	8035572	3000615	SCOP2B (2022-06-29)
A	SCOP2 Family	Glycerophosphoryl diester phosphodiesterase	8023192	4000418	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PLC-like phosphodiesterases	8035572	3000615	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	GDPD	e1zccF1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: GDPD	ECOD (1.6)
E	GDPD	e1zccE1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: GDPD	ECOD (1.6)
D	GDPD	e1zccD1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: GDPD	ECOD (1.6)
C	GDPD	e1zccC1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: GDPD	ECOD (1.6)
B	GDPD	e1zccB1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: GDPD	ECOD (1.6)
A	GDPD	e1zccA1	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)
F	3.20.20.190	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphatidylinositol (PI) phosphodiesterase	CATH (4.3.0)
E	3.20.20.190	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphatidylinositol (PI) phosphodiesterase	CATH (4.3.0)
D	3.20.20.190	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphatidylinositol (PI) phosphodiesterase	CATH (4.3.0)
C	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)
A	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, C, D, E A, B, C, D, E, F	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, C, D, E A, B, C, D, E, F	glycerophosphodiester phosphodiesterase	phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds phosphoric diester hydrolase activity hydrolase activity catalytic activity	primary metabolic process metabolic process cellular process lipid metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR030395	Glycerophosphodiester phosphodiesterase domain	Domain
A, B, C, D, E A, B, C, D, E, F	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.