8DCM

Crystal structure of Clostridioides difficile binary toxin proCDTb lacking D4 in complex with BINTOXB/22 Fab

External Resource: Annotation

Domain Annotation: ECOD Classification
SAbDab Antibody Annotation
Protein Family 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)
A	PF07654	e8dcmA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
A	PF07686	e8dcmA2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
B	PF07654	e8dcmB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
B	PF07686	e8dcmB2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A	Heavy Chain	IGHV9	-	adp-ribosylating binary toxin binding subunit cdtb	SAbDab (2024-05-10)
B	Light Chain	IGKV6	Kappa	adp-ribosylating binary toxin binding subunit cdtb	SAbDab (2024-05-10)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C	PF07691	PA14 domain (PA14)	PA14 domain	This domain forms an insert in bacterial beta-glucosidases and is found in other glycosidases, glycosyltransferases, proteases, amidases, yeast adhesins, and bacterial toxins, including anthrax protective antigen (PA). The domain also occurs in a Dic ...	This domain forms an insert in bacterial beta-glucosidases and is found in other glycosidases, glycosyltransferases, proteases, amidases, yeast adhesins, and bacterial toxins, including anthrax protective antigen (PA). The domain also occurs in a Dictyostelium prespore-cell-inducing factor Psi and in fibrocystin, the mammalian protein whose mutation leads to polycystic kidney and hepatic disease. The crystal structure of PA shows that this domain (named PA14 after its location in the PA20 pro-peptide) has a beta-barrel structure. The PA14 domain sequence suggests a binding function, rather than a catalytic role. The PA14 domain distribution is compatible with carbohydrate binding.	Domain
C	PF17475	Clostridial binary toxin B/anthrax toxin PA domain 2 (Binary_toxB_2)	Clostridial binary toxin B/anthrax toxin PA domain 2	This domain forms the middle beta sandwish domain in anthrax toxin.	Domain
C	PF17476	Clostridial binary toxin B/anthrax toxin PA domain 3 (Binary_toxB_3)	Clostridial binary toxin B/anthrax toxin PA domain 3	This entry represents the beta-grasp domain in anthrax protective antigen.	Domain
C	PF03495	Clostridial binary toxin B/anthrax toxin PA Ca-binding domain (Binary_toxB)	Clostridial binary toxin B/anthrax toxin PA Ca-binding domain	This domain is a calcium binding domain in the anthrax toxin protective antigen.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	BINTOXB/22 Fab heavy chain	-	-	-
B	BINTOXB/22 Fab light chain	-	-	-
C	ADP-ribosylating binary toxin binding subunit CdtB	transferase activity catalytic activity identical protein binding protein binding 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	extracellular region cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR035331	Clostridial binary toxin B/anthrax toxin PA, domain 3	Domain
C	IPR011658	PA14 domain	Domain
C	IPR027439	Protective antigen, heptamerisation domain	Domain
C	IPR035088	Protective antigen, Ca-binding domain	Domain
C	IPR037149	Protective antigen, heptamerisation domain superfamily	Homologous Superfamily
C	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 R01GM133198.