› 8ybn

X-ray diffraction
2.18Å resolution

Crystal structure of nanobody SEB-Nb8 bound to staphylococcal enterotoxin B (SEB)

Released:
DOI: 10.2210/pdb8ybn/pdb
Model geometry
Fit model/data
PDB entry 8ybn coloured by chain, front view.
PDB entry 8ybn coloured by chain, side view.
PDB entry 8ybn coloured by chain, top view.
Source organisms:
Primary publication:
Structural insights into the binding of nanobodies to the Staphylococcal enterotoxin B.
Zong X, Liu P, Wang Z, Zhu H, Zhong C, Zhong P, Jiang H, Liu J, Ma Z, Liu X, Liu R, Ding Y
Int J Biol Macromol 276 133957 (2024)
PMID: 39029852

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-283177 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Enterotoxin type B Chain: A
Molecule details ›
Chain: A
Length: 240 amino acids
Theoretical weight: 28.54 KDa
Source organism: Staphylococcus aureus
Expression system: Escherichia coli
UniProt:
  • Canonical: P01552 (Residues: 28-266; Coverage: 100%)
Gene name: entB
Sequence domains:
nanobody SEB-Nb8 Chain: B
Molecule details ›
Chain: B
Length: 131 amino acids
Theoretical weight: 14.43 KDa
Source organism: Vicugna pacos
Expression system: Escherichia coli

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SSRF BEAMLINE BL10U2
Spacegroup: P212121
Unit cell:
a: 44.967Å b: 87.86Å c: 95.581Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.235 0.232 0.281
Expression system: Escherichia coli

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