3BVT

GOLGI MANNOSIDASE II D204A catalytic nucleophile mutant complex with Methyl (alpha-D-mannopyranosyl)-(1->3)-S-alpha-D-mannopyranoside

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	d3bvta1	All alpha proteins	immunoglobulin/albumin-binding domain-like	Families 57/38 glycoside transferase middle domain	alpha-mannosidase, domain 2	Golgi alpha-mannosidase II	Fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)
A	d3bvta2	All beta proteins	Supersandwich	Galactose mutarotase-like	alpha-mannosidase, C-terminal domain	Golgi alpha-mannosidase II	Fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)
A	d3bvta3	Alpha and beta proteins (a/b)	7-stranded beta/alpha barrel	Glycoside hydrolase/deacetylase	alpha-mannosidase	Golgi alpha-mannosidase II	Fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Families 57/38 glycoside transferase middle domain	8039561	3000997	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Glycoside hydrolase/deacetylase	8039566	3001025	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Galactose mutarotase-like	8039564	3000035	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	KOG1958	e3bvtA6	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: Glycosyl hydrolase domain (From Topology)	T: Glycosyl hydrolase domain	F: KOG1958	ECOD (1.6)
A	KOG1959	e3bvtA5	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: Glycosyl hydrolase domain (From Topology)	T: Glycosyl hydrolase domain	F: KOG1959	ECOD (1.6)
A	Glyco_hydro_38C_1st_1	e3bvtA4	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: supersandwich (From Topology)	T: supersandwich	F: Glyco_hydro_38C_1st_1	ECOD (1.6)
A	Alpha-mann_mid	e3bvtA2	A: alpha bundles	X: immunoglobulin/albumin-binding domain-like	H: Families 57/38 glycoside transferase middle domain (From Topology)	T: Families 57/38 glycoside transferase middle domain	F: Alpha-mann_mid	ECOD (1.6)
A	Glyco_hydro_38	e3bvtA3	A: a/b barrels	X: TIM beta/alpha-barrel	H: Glycoside hydrolase/deacetylase (From Topology)	T: Glycoside hydrolase/deacetylase	F: Glyco_hydro_38	ECOD (1.6)

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	2.60.40.1180	Mainly Beta	Sandwich	Immunoglobulin-like	Golgi alpha-mannosidase II	CATH (4.3.0)
A	2.70.98.30	Mainly Beta	Distorted Sandwich	Beta-galactosidase	Chain A, domain 5	CATH (4.3.0)
A	2.60.40.1360	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF18230	Glycosyl hydrolases family 38 C-terminal sub-domain (Glyc_hyd_38C_2)	Glycosyl hydrolases family 38 C-terminal sub-domain	This is a subdomain found in the C-terminal region of golgi alpha-mannosidase II present in Drosophila melanogaster. These proteins are important in glycoprotein processing and are thought to cleave mannosidic bonds through a double displacement mech ...	This is a subdomain found in the C-terminal region of golgi alpha-mannosidase II present in Drosophila melanogaster. These proteins are important in glycoprotein processing and are thought to cleave mannosidic bonds through a double displacement mechanism involving a reaction intermediate.This subdomain is found at the C-terminal of Glycosyl hydrolases family 38 C-terminal domain [1].	Domain
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	PF09261	Alpha mannosidase middle domain (Alpha-mann_mid)	Alpha mannosidase middle domain	Members of this family adopt a structure consisting of three alpha helices, in an immunoglobulin/albumin-binding domain-like fold. They are predominantly found in the enzyme alpha-mannosidase [1].	Domain
A	PF21260	Lysosomal alpha-mannosidase-like, central domain (Laman-like_dom)	Lysosomal alpha-mannosidase-like, central domain	This domain is found in Lysosomal alpha-mannosidase from Bos taurus (Laman) and similar proteins from eukaryotes. This protein is necessary for the catabolism of N-linked carbohydrates released during glycoprotein turnover. Laman, which belongs to th ...	This domain is found in Lysosomal alpha-mannosidase from Bos taurus (Laman) and similar proteins from eukaryotes. This protein is necessary for the catabolism of N-linked carbohydrates released during glycoprotein turnover. Laman, which belongs to the glycoside hydrolase family 38 (GH38), is organised into four domains: the alpha-beta N-terminal Pfam:PF01074, a three-helix bundle domain Pfam:PF09261, and three mainly beta-sheet domains (covered by this entry, Pfam:PF07748 and Pfam:PF17677) [1-5].	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Alpha-mannosidase 2	hydrolase activity, acting on glycosyl bonds hydrolase activity, hydrolyzing O-glycosyl compounds mannosidase activity hydrolase activity catalytic activity alpha-mannosidase activity mannosyl-oligosaccharide mannosidase activity mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity binding carbohydrate binding cation binding ion binding metal ion binding small molecule binding	pigment metabolic process eye pigmentation developmental pigmentation pigment biosynthetic process primary metabolic process macromolecule biosynthetic process pigmentation pigment metabolic process involved in pigmentation eye pigment metabolic process rhodopsin metabolic process biosynthetic process rhodopsin biosynthetic process pigment metabolic process involved in developmental pigmentation metabolic process pigment metabolic process eye pigmentation developmental pigmentation pigment biosynthetic process primary metabolic process macromolecule biosynthetic process pigmentation pigment metabolic process involved in pigmentation eye pigment metabolic process rhodopsin metabolic process biosynthetic process rhodopsin biosynthetic process pigment metabolic process involved in developmental pigmentation metabolic process cellular process protein metabolic process macromolecule metabolic process eye pigment biosynthetic process carbohydrate derivative metabolic process N-glycan processing glycoprotein metabolic process carbohydrate derivative biosynthetic process glycoprotein biosynthetic process protein glycosylation glycosylation macromolecule modification macromolecule glycosylation protein modification process encapsulation of foreign target immune system process immune effector process monosaccharide metabolic process carbohydrate metabolic process mannose metabolic process hexose metabolic process small molecule metabolic process	membrane-bounded organelle intracellular anatomical structure Golgi apparatus subcompartment Golgi apparatus organelle subcompartment intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure organelle Golgi stack cytoplasm Golgi membrane membrane membrane-bounded organelle intracellular anatomical structure Golgi apparatus subcompartment Golgi apparatus organelle subcompartment intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure organelle Golgi stack cytoplasm Golgi membrane membrane bounding membrane of organelle organelle membrane endoplasmic reticulum

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR015341	Glycoside hydrolase family 38, central domain	Domain
A	IPR041566	Alpha-mannosidase 2, C-terminal sub-domain	Domain
A	IPR013780	Glycosyl hydrolase, all-beta	Homologous Superfamily
A	IPR027291	Glycoside hydrolase 38, N-terminal domain superfamily	Homologous Superfamily
A	IPR037094	Glycoside hydrolase family 38, central domain superfamily	Homologous Superfamily
A	IPR028995	Glycoside hydrolase families 57/38, central domain superfamily	Homologous Superfamily
A	IPR050843	Glycosyl Hydrolase Family 38	Family
A	IPR048534	Lysosomal alpha-mannosidase-like, central domain	Domain
A	IPR011330	Glycoside hydrolase/deacetylase, beta/alpha-barrel	Homologous Superfamily
A	IPR011682	Glycosyl hydrolase family 38, C-terminal	Domain
A	IPR000602	Glycoside hydrolase family 38, N-terminal domain	Domain
A	IPR011013	Galactose mutarotase-like 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.