Annotations: 3GDB

Crystal structure of Spr0440 glycoside hydrolase domain, Endo-D from Streptococcus pneumoniae R6

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	GH85 catalytic domain-like	8044662	4004066	SCOP2 (2022-06-29)
A	SCOP2 Family	GH85 putative CBM-like	8051927	4007574	SCOP2 (2022-06-29)
A	SCOP2 Family	Fibronectin type III	8051929	4007555	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	(Trans)glycosidases	8051926	3000313	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	galactose-binding domain-like	8051928	3000087	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Fibronectin type III	8051930	3002063	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		e3gdbA1	A: beta barrels	X: PH domain-like	H: PH domain-like	T: PH domain-like	F:	ECOD (v294.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
A	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (4.3.0)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF21910	GH85 endohexosaminidases, C-terminal domain (GH85_C)	GH85 endohexosaminidases, C-terminal domain	This entry represents the C-terminal domain of GH85 endohexosaminidases.These enzymes cleave the glycosidic linkage between the two N-acetylglucosamine units that make up the chitobiose core of N-glycans. The C-terminal domain adopts a typical fibron ...	This entry represents the C-terminal domain of GH85 endohexosaminidases.These enzymes cleave the glycosidic linkage between the two N-acetylglucosamine units that make up the chitobiose core of N-glycans. The C-terminal domain adopts a typical fibronectin Ig-like fold [1].	Domain
A	PF03644	Glycosyl hydrolase family 85 (Glyco_hydro_85)	Glycosyl hydrolase family 85	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Putative uncharacterized protein spr0440	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity hydrolase activity, acting on glycosyl bonds hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity catalytic activity	carbohydrate derivative biosynthetic process glycoprotein biosynthetic process carbohydrate derivative metabolic process primary metabolic process N-glycan processing glycoprotein metabolic process macromolecule biosynthetic process protein N-linked glycosylation biosynthetic process metabolic process cellular process protein metabolic process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR032979	Cytosolic endo-beta-N-acetylglucosaminidase	Family
A	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A	IPR005877	YSIRK Gram-positive signal peptide	Domain
A	IPR011098	G5 domain	Domain
A	IPR005201	Cytosolic endo-beta-N-acetylglucosaminidase, TIM barrel domain	Domain
A	IPR054110	Endo-beta-N-acetylglucosaminidase D-like, D2 domain	Domain
A	IPR022038	Ig-like domain, bacterial type	Domain
A	IPR019931	LPXTG cell wall anchor motif	Conserved Site

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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.