6OQ8

Structure of the GTD domain of Clostridium difficile toxin B in complex with VHH 7F

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
SAbDab Antibody Annotation
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	d6oq8a1	Alpha and beta proteins (a/b)	Nucleotide-diphospho-sugar transferases	Nucleotide-diphospho-sugar transferases	Glycosylating toxin catalytic domain-like	automated matches	(Clostridioides difficile ) [TaxId: 1496 ],	SCOPe (2.08)
A	d6oq8a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Clostridioides difficile ) [TaxId: 1496 ],	SCOPe (2.08)
C [auth B]	d6oq8b1	Alpha and beta proteins (a/b)	Nucleotide-diphospho-sugar transferases	Nucleotide-diphospho-sugar transferases	Glycosylating toxin catalytic domain-like	automated matches	(Clostridioides difficile ) [TaxId: 1496 ],	SCOPe (2.08)
C [auth B]	d6oq8b2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Clostridioides difficile ) [TaxId: 1496 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Nucleotide-diphospho-sugar transferases	8033597	3000077	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Nucleotide-diphospho-sugar transferases	8033597	3000077	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	MLD	e6oq8A2	A: alpha bundles	X: Bromodomain-like	H: PMT helical bundle domain-like	T: PMT helical bundle domain-like	F: MLD	ECOD (1.6)
A	TcdA_TcdB	e6oq8A1	A: a/b three-layered sandwiches	X: Nucleotide-diphospho-sugar transferases (From Topology)	H: Nucleotide-diphospho-sugar transferases (From Topology)	T: Nucleotide-diphospho-sugar transferases	F: TcdA_TcdB	ECOD (1.6)
C [auth B]	MLD	e6oq8B1	A: alpha bundles	X: Bromodomain-like	H: PMT helical bundle domain-like	T: PMT helical bundle domain-like	F: MLD	ECOD (1.6)
C [auth B]	TcdA_TcdB	e6oq8B2	A: a/b three-layered sandwiches	X: Nucleotide-diphospho-sugar transferases (From Topology)	H: Nucleotide-diphospho-sugar transferases (From Topology)	T: Nucleotide-diphospho-sugar transferases	F: TcdA_TcdB	ECOD (1.6)
D [auth C]	V-set_8	e6oq8C1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
B [auth D]	V-set_8	e6oq8D1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.58.1190	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (utative)
A	1.10.10.1780	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		CATH (utative)
C [auth B]	1.20.58.1190	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (utative)
C [auth B]	1.10.10.1780	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		CATH (utative)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth D], D [auth C]	Heavy Chain	IGHV1	-	toxin b	SAbDab (2024-11-08)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth B]	PF12919	TcdA/TcdB catalytic glycosyltransferase domain (TcdA_TcdB)	TcdA/TcdB catalytic glycosyltransferase domain	This domain represents the N-terminal glycosyltransferase from a set of toxins found in some bacteria. This domain in TcdB glycosylates the host RhoA protein.	Domain
A, C [auth B]	PF12918	TcdB toxin N-terminal helical domain (TcdB_N)	TcdB toxin N-terminal helical domain	This is a short helical bundle domain found associated with the catalytic domain of the TcdB toxin from C. difficile [1]. The function of this domain is unknown, but it may be involved in substrate recognition.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C [auth B]	Toxin B	binding lipid binding toxin activity glycosyltransferase activity transferase activity glucosyltransferase activity hexosyltransferase activity catalytic activity cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity cation binding ion binding binding lipid binding toxin activity glycosyltransferase activity transferase activity glucosyltransferase activity hexosyltransferase activity catalytic activity cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity cation binding ion binding metal ion binding small molecule binding	proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	membrane cellular anatomical entity extracellular region host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane host cell cytoplasm part host intracellular organelle host cell endosome membrane host cell cytoplasm host cell part host cell endosome host intracellular region membrane cellular anatomical entity extracellular region host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane host cell cytoplasm part host intracellular organelle host cell endosome membrane host cell cytoplasm host cell part host cell endosome host intracellular region host cell plasma membrane host cell cytosol
B [auth D], D [auth C]	7F	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth B]	IPR038383	CGT/MARTX, cysteine protease (CPD) domain superfamily	Homologous Superfamily
A, C [auth B]	IPR024772	TcdA/TcdB toxin, N-terminal helical domain	Domain
A, C [auth B]	IPR020974	CGT/MARTX, cysteine protease (CPD) domain	Domain
A, C [auth B]	IPR024769	TcdA/TcdB toxin, pore forming domain	Domain
A, C [auth B]	IPR029044	Nucleotide-diphospho-sugar transferases	Homologous Superfamily
A, C [auth B]	IPR024770	TcdA/TcdB toxin, catalytic glycosyltransferase domain	Domain
A, C [auth B]	IPR018337	Cell wall/choline-binding repeat	Repeat

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.