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

X-ray diffraction
2.44Å resolution
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:
Assembly composition:
hetero dimer (preferred)
Entry contents: 3 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: SabA N-terminal extracellular adhesion domain-containing protein and IG-heavy chain
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Multimeric state: hetero dimer
Accessible surface area: 23940.12 Å2
Buried surface area: 3751.15 Å2
Dissociation area: 910.55 Å2
Dissociation energy (ΔGdiss): 0.02 kcal/mol
Dissociation entropy (TΔSdiss): 11.99 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-219132
Assembly 2
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Assembly Name: SabA N-terminal extracellular adhesion domain-containing protein and IG-heavy chain
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Multimeric state: hetero dimer
Accessible surface area: 24325.24 Å2
Buried surface area: 3737.01 Å2
Dissociation area: 897.58 Å2
Dissociation energy (ΔGdiss): 0.94 kcal/mol
Dissociation entropy (TΔSdiss): 11.99 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-219132

Macromolecules

SabA N-terminal extracellular adhesion domain-containing protein
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
Pfam: SabA N-terminal extracellular adhesion domain
InterPro: SabA, N-terminal extracellular adhesion domain
SabA N-terminal extracellular adhesion domain-containing protein in PDB entry 5f7y, assembly 1, front view.
SabA N-terminal extracellular adhesion domain-containing protein in PDB entry 5f7y, assembly 1, side view.
SabA N-terminal extracellular adhesion domain-containing protein in PDB entry 5f7y, assembly 1, top view.
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SabA N-terminal extracellular adhesion domain-containing protein
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
Pfam: SabA N-terminal extracellular adhesion domain
InterPro: SabA, N-terminal extracellular adhesion domain
SabA N-terminal extracellular adhesion domain-containing protein in PDB entry 5f7y, assembly 2, front view.
SabA N-terminal extracellular adhesion domain-containing protein in PDB entry 5f7y, assembly 2, side view.
SabA N-terminal extracellular adhesion domain-containing protein in PDB entry 5f7y, assembly 2, top view.
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Nanobody Nb-ER19
Chains: C, D
Length: 120 amino acids
Theoretical weight: 13.26 KDa
Source organism: Lama glama
Expression system: Escherichia coli
InterPro:
CATH: Immunoglobulins
Nanobody Nb-ER19 in PDB entry 5f7y, assembly 1, front view.
Nanobody Nb-ER19 in PDB entry 5f7y, assembly 1, side view.
Nanobody Nb-ER19 in PDB entry 5f7y, assembly 1, top view.
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