Skip to main content

 8YBM | pdb_00008ybm

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

External Resource: Annotation


Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
DUCR_hingee8ybmD1 A: alpha arraysX: Hypothetical protein YqbG-likeH: Hypothetical protein YqbG-likeT: alpha/beta-HydrolasesF: UCR_hingeECOD (v295.2)
BLRR_1, LRR_5, LRR_6, LRR_8e8ybmB01 A: alpha arraysX: Hypothetical protein YqbG-likeH: Hypothetical protein YqbG-likeT: alpha/beta-HydrolasesF: LRR_1, LRR_5, LRR_6, LRR_8ECOD (v295.2)
CUCR_hingee8ybmC1 A: alpha arraysX: Hypothetical protein YqbG-likeH: Hypothetical protein YqbG-likeT: alpha/beta-HydrolasesF: UCR_hingeECOD (v295.2)
AUCR_hingee8ybmA1 A: alpha arraysX: Hypothetical protein YqbG-likeH: Hypothetical protein YqbG-likeT: alpha/beta-HydrolasesF: UCR_hingeECOD (v295.2)

SAbDab Antibody Annotation SAbDab Database Homepage

ChainChain ClassChain SubclassChain TypeAntigen Name(s) Provenance Source
B, D
Heavy ChainIGHV1 -enterotoxin type bSAbDab (2026-10-16)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
B, D
nanobody SEB-Nb6---
A, C
Enterotoxin type B -

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A, C
IPR006123Staphylococcal/Streptococcal toxin, beta-grasp domainDomain
A, C
IPR006177Staphylococcal/streptococcal toxin, bacterialFamily
A, C
IPR006126Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved siteConserved Site
A, C
IPR016091Superantigen toxin, C-terminalHomologous Superfamily
A, C
IPR006173Staphylococcal/Streptococcal toxin, OB-foldDomain
A, C
IPR013307Superantigen, staphylococcal/streptococcal toxin, bacterialFamily
A, C
IPR008992EnterotoxinHomologous Superfamily