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)
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)
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)
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)
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)
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)
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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Glycerophosphoryl diester phosphodiesterase	8023192	4000418	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PLC-like phosphodiesterases	8035572	3000615	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	PLC-like phosphodiesterases	8035572	3000615	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PLC-like phosphodiesterases	8035572	3000615	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	PLC-like phosphodiesterases	8035572	3000615	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	PLC-like phosphodiesterases	8035572	3000615	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	PLC-like phosphodiesterases	8035572	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	e1zccA1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: GDPD	ECOD (v294.1)
B	Sigma_1_2	e1zccB1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: Sigma_1_2	ECOD (v294.1)
C	PF27526	e1zccC1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: PF27526	ECOD (v294.1)
D	Sigma_1_2	e1zccD1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: Sigma_1_2	ECOD (v294.1)
E	PF27526	e1zccE1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: PF27526	ECOD (v294.1)
F	PF27526	e1zccF1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: PF27526	ECOD (v294.1)

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)
C	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)
E	3.20.20.190	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphatidylinositol (PI) phosphodiesterase	CATH (4.3.0)
F	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.