› 5f9d

X-ray diffraction
2.59Å resolution

Blood group antigen binding adhesin BabA of Helicobacter pylori strain P436 in complex with Lewis b blood group B heptasaccharide

Released:
DOI: 10.2210/pdb5f9d/pdb
Model geometry
Fit model/data
PDB entry 5f9d coloured by chain, front view.
PDB entry 5f9d coloured by chain, side view.
PDB entry 5f9d 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-208099 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (3 distinct):
SabA N-terminal extracellular adhesion domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 463 amino acids
Theoretical weight: 48.9 KDa
Source organism: Helicobacter pylori
Expression system: Escherichia coli
UniProt:
  • Canonical: O52269 (Residues: 45-200, 278-480; Coverage: 50%)
  • Canonical: Q6DT10 (Residues: 50-123; Coverage: 30%)
Gene names: babA, babA2
Sequence domains: SabA N-terminal extracellular adhesion domain
Nanobody Nb-ER19 Chain: C
Molecule details ›
Chain: C
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: BGC, GAL, NAG, FUC, GLA
Carbohydrate polymer
No bound ligands
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: C2221
Unit cell:
a: 119.18Å b: 135.09Å c: 127.33Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.197 0.195 0.234
Expression system: Escherichia coli

Quick links

Citations

22 review citations

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

2 mentions without citation

Conformations of the type-1 lacto-N-biose I unit in protein complex structures.
Fushinobu S. (2018)
1 more