8YBM | pdb_00008ybm

Crystal structure of nanobody SEB-Nb6 bound to staphylococcal enterotoxin B (SEB)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
SAbDab Antibody Annotation
Protein Family 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)
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)
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)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B, D	Heavy Chain	IGHV1	-	enterotoxin type b	SAbDab (2025-12-19)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF01123	Staphylococcal/Streptococcal toxin, OB-fold domain (Stap_Strp_toxin)	Staphylococcal/Streptococcal toxin, OB-fold domain	This entry represents an OB-fold domain found in enterotoxins.	Domain
A, C	PF02876	Staphylococcal/Streptococcal toxin, beta-grasp domain (Stap_Strp_tox_C)	Staphylococcal/Streptococcal toxin, beta-grasp domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	Enterotoxin type B	cation binding ion binding binding metal ion binding small molecule binding toxin activity	-	cellular anatomical structure extracellular region
B, D	nanobody SEB-Nb6	-	-	-

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.