› 5f7y

X-ray diffraction
2.44Å resolution

Blood group antigen binding adhesin BabA of Helicobacter pylori strain 17875 in complex with blood group A type-1 hexasaccharide

Released:
DOI: 10.2210/pdb5f7y/pdb
PDB entry 5f7y coloured by chain, front view.
PDB entry 5f7y coloured by chain, side view.
PDB entry 5f7y coloured by chain, top view.
Source organisms:
Primary publication:
Structural Insights into Polymorphic ABO Glycan Binding by Helicobacter pylori.
Moonens K, Gideonsson P, Subedi S, Bugaytsova J, Romaõ E, Mendez M, Nordén J, Fallah M, Rakhimova L, Shevtsova A, Lahmann M, Castaldo G, Brännström K, Coppens F, Lo AW, Ny T, Solnick JV, Vandenbussche G, Oscarson S, Hammarström L, Arnqvist A, Berg DE, Muyldermans S, Borén T, Remaut H
Cell Host Microbe 19 55-66 (2016)
PMID: 26764597

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-219132 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (4 distinct):
SabA N-terminal extracellular adhesion domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 466 amino acids
Theoretical weight: 49.4 KDa
Source organism: Helicobacter pylori
Expression system: Escherichia coli
UniProt:
  • Canonical: O52269 (Residues: 45-480; Coverage: 61%)
Gene name: babA2
Sequence domains: SabA N-terminal extracellular adhesion domain
SabA N-terminal extracellular adhesion domain-containing protein Chain: B
Molecule details ›
Chain: B
Length: 466 amino acids
Theoretical weight: 49.37 KDa
Source organism: Helicobacter pylori
Expression system: Escherichia coli
UniProt:
  • Canonical: O52269 (Residues: 45-480; Coverage: 61%)
Gene name: babA2
Sequence domains: SabA N-terminal extracellular adhesion domain
Nanobody Nb-ER19 Chains: C, D
Molecule details ›
Chains: C, D
Length: 120 amino acids
Theoretical weight: 13.26 KDa
Source organism: Lama glama
Expression system: Escherichia coli
Structure domains: Immunoglobulins

Ligands and Environments

Carbohydrate polymer : NEW Components: GLC, GAL, NAG, FUC, A2G
Carbohydrate polymer
No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: P21
Unit cell:
a: 50.87Å b: 131.71Å c: 123.61Å
α: 90° β: 94.69° γ: 90°
R-values:
R R work R free
0.177 0.176 0.205
Expression system: Escherichia coli

Quick links

Citations

22 review citations

Pathogenesis of Helicobacter pylori infection.
Backert et al. (2016)
21 more

1 mention without citation

ClusPro in rounds 38 to 45 of CAPRI: Toward combining template-based methods with free docking.
Padhorny et al. (2020)