› 7xli

X-ray diffraction
1.7Å resolution

Crystal structure of IsdB linker-NEAT2 bound to a nanobody (VHH)

Released:
DOI: 10.2210/pdb7xli/pdb
PDB entry 7xli coloured by chain, front view.
PDB entry 7xli coloured by chain, side view.
PDB entry 7xli coloured by chain, top view.
Source organisms:
Primary publication:
Targeting hemoglobin receptors IsdH and IsdB of Staphylococcus aureus with a single VHH antibody inhibits bacterial growth.
Valenciano-Bellido S, Caaveiro JMM, Nakakido M, Kuroda D, Aikawa C, Nakagawa I, Tsumoto K
OpenAccess logo J Biol Chem 299 104927 (2023)
PMID: 37330175

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-573196 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Iron-regulated surface determinant protein B Chain: A
Molecule details ›
Chain: A
Length: 180 amino acids
Theoretical weight: 21.18 KDa
Source organism: Staphylococcus aureus subsp. aureus Mu50
Expression system: Escherichia coli
UniProt:
  • Canonical: Q99UX5 (Residues: 274-453; Coverage: 30%)
Gene names: SAV1129, frpB, isdB, sasJ, sirH
Sequence domains:
VHH6 nanobody Chain: B
Molecule details ›
Chain: B
Length: 134 amino acids
Theoretical weight: 14.97 KDa
Source organism: Lama glama
Expression system: Escherichia coli

Ligands and Environments

2 bound ligands:
Ligand CL 1 x CL
Ligand CA 1 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P212121
Unit cell:
a: 40.321Å b: 48.58Å c: 140.7Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.21 0.209 0.237
Expression system: Escherichia coli

Quick links

Citations

3 citation in other articles

Development of novel humanized VHH synthetic libraries based on physicochemical analyses.
Nakakido et al. (2024)
2 more

1 mention without citation

Targeting hemoglobin receptors IsdH and IsdB of Staphylococcus aureus with a single VHH antibody inhibits bacterial growth.
Valenciano-Bellido et al. (2023)