7UBY

Structure of the GTD domain of Clostridium difficile toxin A in complex with VHH AH3

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth B]	SCOP2B Superfamily	Nucleotide-diphospho-sugar transferases	8099200	3000077	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Nucleotide-diphospho-sugar transferases	8099200	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)
B [auth D]	V-set_12	e7ubyD1	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)
D [auth C]	V-set_12	e7ubyC1	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 [auth B]	MLD	e7ubyB1	A: alpha bundles	X: Bromodomain-like	H: PMT helical bundle domain-like	T: PMT helical bundle domain-like	F: MLD	ECOD (1.6)
A [auth B]	TcdA_TcdB	e7ubyB2	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 A]	MLD	e7ubyA1	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 A]	TcdA_TcdB	e7ubyA2	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)

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	-	glucosyltransferase tcda	SAbDab (2024-11-08)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B], C [auth A]	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 [auth B], C [auth A]	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
B [auth D], D [auth C]	Nanobody VHH AH3	-	-	-
A [auth B], C [auth A]	Glucosyltransferase TcdA	glycosyltransferase activity transferase activity catalytic activity binding lipid binding toxin 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

InterPro: Protein Family Classification InterPro Database Homepage

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