3I10 | pdb_00003i10

Crystal structure of Putative glycerophosphoryl diester phosphodiesterase (NP_812074.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.35 A resolution

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Glycerophosphoryl diester phosphodiesterase	8045501	4000418	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PLC-like phosphodiesterases	8090822	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)
A	GDPD	e3i10A1	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF03009	Glycerophosphoryl diester phosphodiesterase family (GDPD)	Glycerophosphoryl diester phosphodiesterase family	-	Family
A	PF16387	Domain of unknown function (DUF4996)	Domain of unknown function	This domain of around 100 residues locates at the C-terminal of some glycerophosphoryl diester phosphodiesterases and uncharacterized proteins in various Bacteroides and Prevotella species. The function of this domain is not yet clear, however, it i ...	This domain of around 100 residues locates at the C-terminal of some glycerophosphoryl diester phosphodiesterases and uncharacterized proteins in various Bacteroides and Prevotella species. The function of this domain is not yet clear, however, it is described as a putative glycerophosphoryl diester phosphodiesterase (PDBe:3i10).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Putative Glycerophosphoryl diester phosphodiesterase	phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds phosphoric diester hydrolase activity glycerophosphodiester phosphodiesterase activity hydrolase activity catalytic activity	amine metabolic process ethanolamine metabolic process metabolic process cellular process alcohol metabolic process small molecule metabolic process primary alcohol metabolic process phospholipid metabolic process organophosphate metabolic process phosphate-containing compound metabolic process primary metabolic process phosphorus metabolic process lipid metabolic process N-acylethanolamine metabolic process	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR032160	Domain of unknown function DUF4996	Domain
A	IPR030395	Glycerophosphodiester phosphodiesterase domain	Domain
A	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.