Annotations: 6OQ5

Structure of the full-length Clostridium difficile toxin B in complex with 3 VHHs

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D [auth F]	Lsr2_DNA-bd (DEPRECATED)	e6oq5F1	A: alpha arrays	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Lsr2_DNA-bd (DEPRECATED)	ECOD (v295.2)
C [auth E]	Lsr2_DNA-bd (DEPRECATED)	e6oq5E1	A: alpha arrays	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Lsr2_DNA-bd (DEPRECATED)	ECOD (v295.2)
B [auth D]	Lsr2_DNA-bd (DEPRECATED)	e6oq5D1	A: alpha arrays	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Lsr2_DNA-bd (DEPRECATED)	ECOD (v295.2)
A		e6oq5A6	A: alpha arrays	X: Mog1p/PsbP-like	H: Nucleotidyltransferase	T: Nucleotidyltransferase	F:	ECOD (v295.2)
A	BamI_lipocalin	e6oq5A1	A: alpha arrays	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: Family A G protein-coupled receptor-like	F: BamI_lipocalin	ECOD (v295.2)
A	HORMA	e6oq5A3	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: HORMA	ECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.10.1780	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		CATH (utative)
A	3.40.50.11050	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	MARTX cysteine protease (CPD) domain	CATH (utative)
A	2.10.270.10	Mainly Beta	Ribbon	left handed beta-beta-3-solenoid	Cholin Binding	CATH (utative)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
D [auth F]	Heavy Chain	IGHV1	-	toxin b	SAbDab (2026-08-21)
B [auth D]	Heavy Chain	IGHV1	-	toxin b	SAbDab (2026-08-21)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth F]	7F	-	-	-
C [auth E]	E3	-	-	-
B [auth D]	5D	-	-	-
A	Toxin B	glycosyltransferase activity transferase activity catalytic activity	-	cellular anatomical structure extracellular region host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane other organism part host cell cytoplasm part host intracellular organelle host cell endosome membrane host cell cytoplasm host cell part host cell endosome host intracellular region cellular anatomical structure extracellular region host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane other organism part 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	IPR038383	CGT/MARTX, cysteine protease (CPD) domain superfamily	Homologous Superfamily
A	IPR024772	TcdA/TcdB toxin, N-terminal helical domain	Domain
A	IPR020974	CGT/MARTX, cysteine protease (CPD) domain	Domain
A	IPR024769	TcdA/TcdB toxin, pore forming domain	Domain
A	IPR029044	Nucleotide-diphospho-sugar transferases	Homologous Superfamily
A	IPR061976	TcsH, C-terminal DRBD	Domain
A	IPR024770	TcdA/TcdB toxin, catalytic glycosyltransferase domain	Domain
A	IPR018337	Cell wall/choline-binding repeat	Repeat

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A	OPM	Monotopic/peripheral	Alpha/Beta monotopic/peripheral	Nucleotide-diphospho-sugar transferases	Glycosylating toxin

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.