8DCN | pdb_00008dcn

Crystal structure of Clostridioides difficile binary toxin CDTb D4 fragment in complex with BINTOXB/9 Fab

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
E	Ion_trans	e8dcnE1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Ion_trans	ECOD (v294.1)
B	Ion_trans	e8dcnB1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Ion_trans	ECOD (v294.1)
D	Ion_trans	e8dcnD1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Ion_trans	ECOD (v294.1)
A	Ion_trans	e8dcnA1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Ion_trans	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B, E	Light Chain	IGKV8	Kappa	adp-ribosylating binary toxin binding subunit cdtb	SAbDab (2026-03-27)
A, D	Heavy Chain	IGHV1	-	adp-ribosylating binary toxin binding subunit cdtb	SAbDab (2026-03-27)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, F	ADP-ribosylating binary toxin binding subunit CdtB	cation binding ion binding binding metal ion binding small molecule binding transferase activity catalytic activity identical protein binding protein binding	cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly protein homooligomerization cellular process cellular component organization or biogenesis	cellular anatomical structure extracellular region
B, E	BINTOXB/9 Fab light chain	-	-	-
A, D	BINTOXB/9 Fab heavy chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, F	IPR035331	Clostridial binary toxin B/anthrax toxin PA, domain 3	Domain
C, F	IPR011658	PA14 domain	Domain
C, F	IPR027439	Protective antigen, heptamerisation domain	Domain
C, F	IPR035088	Protective antigen, Ca-binding domain	Domain
C, F	IPR037149	Protective antigen, heptamerisation domain superfamily	Homologous Superfamily
C, F	IPR003896	Bacterial exotoxin B	Family

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.