5KIJ | pdb_00005kij

Crystal structure of the class I human endoplasmic reticulum 1,2-alpha-mannosidase and Man9GlcNAc2-PA complex

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
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d5kija_	All alpha proteins	alpha/alpha toroid	Seven-hairpin glycosidases	Class I alpha-1	2-mannosidase, catalytic domain	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Seven-hairpin glycosidases	8033654	3000996	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	FXa_inhibition	e5kijA1	A: alpha bundles	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: FXa_inhibition	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.50.10.10	Mainly Alpha	Alpha/alpha barrel	Glycosyltransferase		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01532	Glycosyl hydrolase family 47 (Glyco_hydro_47)	Glycosyl hydrolase family 47	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding mannosyl-oligosaccharide mannosidase activity hydrolase activity, acting on glycosyl bonds mannosyl-oligosaccharide 1,2-alpha-mannosidase activity hydrolase activity, hydrolyzing O-glycosyl compounds mannosidase activity hydrolase activity alpha-mannosidase activity catalytic activity	protein alpha-1,2-demannosylation carbohydrate derivative metabolic process primary metabolic process glycoprotein metabolic process macromolecule modification protein deglycosylation protein demannosylation metabolic process cellular process protein metabolic process macromolecule metabolic process protein modification process endoplasmic reticulum mannose trimming carbohydrate metabolic process protein alpha-1,2-demannosylation carbohydrate derivative metabolic process primary metabolic process glycoprotein metabolic process macromolecule modification protein deglycosylation protein demannosylation metabolic process cellular process protein metabolic process macromolecule metabolic process protein modification process endoplasmic reticulum mannose trimming carbohydrate metabolic process oligosaccharide metabolic process cellular response to stimulus catabolic process response to stimulus proteasomal protein catabolic process protein catabolic process macromolecule catabolic process ERAD pathway cellular response to stress response to chemical response to stress response to endoplasmic reticulum stress carbohydrate derivative biosynthetic process glycoprotein biosynthetic process N-glycan processing macromolecule biosynthetic process protein N-linked glycosylation biosynthetic process viral gene expression viral protein processing viral process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure cytoplasmic vesicle organelle intracellular vesicle cytoplasm intracellular membrane-bounded organelle vesicle endoplasmic reticulum endoplasmic reticulum quality control compartment endomembrane system membrane membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure cytoplasmic vesicle organelle intracellular vesicle cytoplasm intracellular membrane-bounded organelle vesicle endoplasmic reticulum endoplasmic reticulum quality control compartment endomembrane system membrane Golgi apparatus extracellular vesicle extracellular organelle extracellular region extracellular membrane-bounded organelle organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network organelle membrane endoplasmic reticulum membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR050749	Glycosyl Hydrolase Family 47	Family
A	IPR012341	Six-hairpin glycosidase-like superfamily	Homologous Superfamily
A	IPR036026	Seven-hairpin glycosidases	Homologous Superfamily
A	IPR001382	Glycoside hydrolase family 47	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q9UKM7	intellectual disability Rafiq syndrome congenital disorder of glycosylation Mental Retardation, Psychosocial non-syndromic intellectual disability ovarian cancer

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.