8H3Y | pdb_00008h3y

Bacteroide Fragilis Toxin in complex with nanobody 327

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
E [auth F]	V-set_12	e8h3yF1	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 E]	V-set_12	e8h3yE1	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)
C [auth D]	V-set_12	e8h3yD1	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)
F [auth C]	fragilysinNterm	e8h3yC1	A: a+b two layers	X: Fragilysin-3 prodomain-like	H: Fragilysin-3 prodomain (From Topology)	T: Fragilysin-3 prodomain	F: fragilysinNterm	ECOD (1.6)
F [auth C]	Reprolysin	e8h3yC2	A: mixed a+b and a/b	X: Zincin-like	H: Metalloproteases (zincins) catalytic domain (From Topology)	T: Metalloproteases (zincins) catalytic domain	F: Reprolysin	ECOD (1.6)
B	fragilysinNterm	e8h3yB2	A: a+b two layers	X: Fragilysin-3 prodomain-like	H: Fragilysin-3 prodomain (From Topology)	T: Fragilysin-3 prodomain	F: fragilysinNterm	ECOD (1.6)
B	Reprolysin	e8h3yB1	A: mixed a+b and a/b	X: Zincin-like	H: Metalloproteases (zincins) catalytic domain (From Topology)	T: Metalloproteases (zincins) catalytic domain	F: Reprolysin	ECOD (1.6)
A	fragilysinNterm	e8h3yA1	A: a+b two layers	X: Fragilysin-3 prodomain-like	H: Fragilysin-3 prodomain (From Topology)	T: Fragilysin-3 prodomain	F: fragilysinNterm	ECOD (1.6)
A	Reprolysin	e8h3yA2	A: mixed a+b and a/b	X: Zincin-like	H: Metalloproteases (zincins) catalytic domain (From Topology)	T: Metalloproteases (zincins) catalytic domain	F: Reprolysin	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E [auth F]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
D [auth E]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
C [auth D]	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
C [auth D], D [auth E], E [auth F]	Heavy Chain	IGHV1	-	fragilysin	SAbDab (2025-12-05)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, F [auth C]	PF16376	N-terminal domain of fragilysin (fragilysinNterm)	N-terminal domain of fragilysin	N-terminal domain of fragilysin, an extracellular metalloprotease toxin, which is primary virulence factor of B. fragilis, an oportunistic pathogen of human gut. The N-terminal domain of fragilysin inhibits fragilysin and is cleaved in a matur ...	N-terminal domain of fragilysin, an extracellular metalloprotease toxin, which is primary virulence factor of B. fragilis, an oportunistic pathogen of human gut. The N-terminal domain of fragilysin inhibits fragilysin and is cleaved in a mature, virulent form.	Domain
A, B, F [auth C]	PF13688	Metallo-peptidase family M12 (Reprolysin_5)	Metallo-peptidase family M12	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth D], D [auth E], E [auth F]	Nanobody 327	-	-	-
A, B, F [auth C]	Fragilysin	peptidase activity catalytic activity, acting on a protein metallopeptidase activity hydrolase activity catalytic activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding toxin activity	proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process symbiont-mediated disruption of host anatomical structure biological process involved in interspecies interaction between organisms symbiont-mediated disruption of host tissue symbiont-mediated disruption of host mucosa disruption of anatomical structure in another organism	cellular anatomical structure extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, F [auth C]	IPR038176	Fragilysin, N-terminal domain superfamily	Homologous Superfamily
A, B, F [auth C]	IPR006026	Peptidase, metallopeptidase	Domain
A, B, F [auth C]	IPR024079	Metallopeptidase, catalytic domain superfamily	Homologous Superfamily
A, B, F [auth C]	IPR032273	Fragilysin, N-terminal	Domain
A, B, F [auth C]	IPR001843	Fragilysin	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.