6XUX | pdb_00006xux

Crystal structure of Megabody Mb-Nb207-cYgjK_NO

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: mpstruc

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	V-set_12	e6xuxA3	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
A	PRK10137	e6xuxA2	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: supersandwich (From Topology)	T: supersandwich	F: PRK10137	ECOD (1.6)
A	Glyco_hydro_63	e6xuxA1	A: alpha superhelices	X: Repetitive alpha hairpins	H: alpha/alpha toroid (From Topology)	T: alpha/alpha toroid	F: Glyco_hydro_63	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.70.98.50	Mainly Beta	Distorted Sandwich	Beta-galactosidase	Chain A, domain 5	CATH (utative)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A	Heavy Chain	IGHV1	-	-	SAbDab (2025-11-28)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF21152	Glucosidase YgjK, N-terminal (YgjK_N)	Glucosidase YgjK, N-terminal	This domain is found at the N-terminal end of Glucosidase YgjK from Escherichia coli and similar bacterial enzymes from the glycoside hydrolase family 63 (GH63) from bacteria, archaea, and eukaryotes. YgjK is organised into N- and A- domains and a li ...	This domain is found at the N-terminal end of Glucosidase YgjK from Escherichia coli and similar bacterial enzymes from the glycoside hydrolase family 63 (GH63) from bacteria, archaea, and eukaryotes. YgjK is organised into N- and A- domains and a linker between them. This entry includes the N-domain and the linker. The N-domain is composed of 18 antiparallel beta-strands divided into two beta- sheets and is classified as a super-beta-sandwich. The linker is composed of two helices and produces a significant curvature between the two domains [1-3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Nanobody,Glucosidase YgjK,Glucosidase YgjK,Nanobody	hydrolase activity, acting on glycosyl bonds alpha,alpha-trehalase activity hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity trehalase activity catalytic activity glucosidase activity cation binding ion binding binding metal ion binding small molecule binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process carbohydrate metabolic process trehalose catabolic process catabolic process trehalose metabolic process oligosaccharide catabolic process oligosaccharide metabolic process carbohydrate catabolic process primary metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process carbohydrate metabolic process trehalose catabolic process catabolic process trehalose metabolic process oligosaccharide catabolic process oligosaccharide metabolic process carbohydrate catabolic process primary metabolic process disaccharide metabolic process metabolic process disaccharide catabolic process	protein-containing complex catalytic complex glucosidase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR012341	Six-hairpin glycosidase-like superfamily	Homologous Superfamily
A	IPR048450	Glucosidase YgjK, N-terminal domain	Domain
A	IPR054491	Mannosylglycerate hydrolase MGH1-like, glycoside hydrolase domain	Domain
A	IPR001661	Glycoside hydrolase, family 37	Family
A	IPR008928	Six-hairpin glycosidase superfamily	Homologous Superfamily

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Cys-Loop Receptor Family	GABA_A receptor (β3 homopentamer) in complex with histamine and megabody Mb25

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.