3LVT | pdb_00003lvt

The Crystal Structure of a Protein in the Glycosyl Hydrolase Family 38 from Enterococcus faecalis to 2.55A

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	DNA_methylase	e3lvtA1	A: a/b three-layered sandwiches	X: YrdC/RibB	H: SH3	T: SH3	F: DNA_methylase	ECOD (v294.1)
A	Sua5_yciO_yrdC	e3lvtA3	A: a/b three-layered sandwiches	X: YrdC/RibB	H: YrdC/RibB	T: YrdC/RibB	F: Sua5_yciO_yrdC	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.20.110.10	Alpha Beta	Alpha-Beta Barrel	7-stranded beta/alpha barrel	Glycoside hydrolase 38, N terminal domain	CATH (4.3.0)
A	1.20.1270.50	Mainly Alpha	Up-down Bundle	Substrate Binding Domain Of Dnak	Chain:A	CATH (4.3.0)
A	2.60.40.2210	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
A	2.70.98.30	Mainly Beta	Distorted Sandwich	Beta-galactosidase	Chain A, domain 5	CATH (4.3.0)
A	2.60.40.2220	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01074	Glycosyl hydrolases family 38 N-terminal domain (Glyco_hydro_38N)	Glycosyl hydrolases family 38 N-terminal domain	Glycosyl hydrolases are key enzymes of carbohydrate metabolism.	Domain
A	PF17677	Glycosyl hydrolases family 38 C-terminal beta sandwich domain (Glyco_hydro38C2)	Glycosyl hydrolases family 38 C-terminal beta sandwich domain	This domain is found at the C-terminal end of various glycosyl hydrolases belonging to family 38. The domain has a beta sandwich fold.	Domain
A	PF07748	Glycosyl hydrolases family 38 C-terminal domain (Glyco_hydro_38C)	Glycosyl hydrolases family 38 C-terminal domain	Glycosyl hydrolases are key enzymes of carbohydrate metabolism.	Domain
A	PF18438	Glycosyl hydrolases family 38 C-terminal domain 1 (Glyco_hydro_38)	Glycosyl hydrolases family 38 C-terminal domain 1	The enzymatic hydrolysis of alpha-mannosides is catalyzed by glycoside hydrolases (GH), termed alpha-mannosidases. Streptococcal (Sp) GH38 alpha-mannosidase active on N-glycans and possibly O-glycans. SpGH38 structure can be considered as five domain ...	The enzymatic hydrolysis of alpha-mannosides is catalyzed by glycoside hydrolases (GH), termed alpha-mannosidases. Streptococcal (Sp) GH38 alpha-mannosidase active on N-glycans and possibly O-glycans. SpGH38 structure can be considered as five domains: an N-terminal alpha/beta-domain, a three-helix bundle and three predominantly beta-sheet domains. This is the first of the three beta-sheet domains found in GH38, termed Beta-1. Structural analysis indicate that the beta-1 domain bows outward from the protein core, is involved in dimer interactions whilst also forming a lid 'above' and somewhat into the active centre of its dimer [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Glycosyl hydrolase, family 38	binding carbohydrate binding hydrolase activity, acting on glycosyl bonds hydrolase activity, hydrolyzing O-glycosyl compounds mannosidase activity hydrolase activity alpha-mannosidase activity catalytic activity cation binding ion binding metal ion binding small molecule binding	monosaccharide metabolic process carbohydrate metabolic process mannose metabolic process hexose metabolic process small molecule metabolic process metabolic process cellular process primary metabolic process catabolic process oligosaccharide catabolic process oligosaccharide metabolic process carbohydrate catabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR028995	Glycoside hydrolase families 57/38, central domain superfamily	Homologous Superfamily
A	IPR015341	Glycoside hydrolase family 38, central domain	Domain
A	IPR011330	Glycoside hydrolase/deacetylase, beta/alpha-barrel	Homologous Superfamily
A	IPR041509	Glycosyl hydrolases 38, beta-1 domain	Domain
A	IPR011682	Glycosyl hydrolase family 38, C-terminal	Domain
A	IPR041147	Glycosyl hydrolases family 38, C-terminal domain	Domain
A	IPR000602	Glycoside hydrolase family 38, N-terminal domain	Domain
A	IPR027291	Glycoside hydrolase 38, N-terminal domain superfamily	Homologous Superfamily
A	IPR011013	Galactose mutarotase-like domain superfamily	Homologous Superfamily
A	IPR037094	Glycoside hydrolase family 38, central 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.