8YBO | pdb_00008ybo

Crystal structure of nanobody SEB-Nb11 bound to staphylococcal enterotoxin B (SEB)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
SAbDab Antibody 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)
C	SCOP2B Superfamily	Bacterial enterotoxins	8041881	3000434	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Superantigen toxins C-terminal domain-like	8034577	3000376	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Bacterial enterotoxins	8041881	3000434	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Superantigen toxins C-terminal domain-like	8034577	3000376	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	LRR_1, LRR_5, LRR_6, LRR_8	e8yboB01	A: a/b three-layered sandwiches	X: ATP-grasp_6	H: ATP-grasp_6	T: ATP-grasp_6	F: LRR_1, LRR_5, LRR_6, LRR_8	ECOD (v294.1)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B, D	Heavy Chain	IGHV3	-	enterotoxin type b	SAbDab (2026-03-27)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	nanobody SEB-Nb11	-	-	-
A, C	Enterotoxin type B	cation binding ion binding binding metal ion binding small molecule binding toxin activity	-	cellular anatomical structure extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR006123	Staphylococcal/Streptococcal toxin, beta-grasp domain	Domain
A, C	IPR006177	Staphylococcal/streptococcal toxin, bacterial	Family
A, C	IPR006126	Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site	Conserved Site
A, C	IPR016091	Superantigen toxin, C-terminal	Homologous Superfamily
A, C	IPR006173	Staphylococcal/Streptococcal toxin, OB-fold	Domain
A, C	IPR013307	Superantigen, staphylococcal/streptococcal toxin, bacterial	Family
A, C	IPR008992	Enterotoxin	Homologous Superfamily

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.