PDB entry 5f93

View 5f93 on RCSB PDB site
Description: Blood group antigen binding adhesin BabA of Helicobacter pylori strain A730 in complex with blood group H Lewis b hexasaccharide
Class: cell adhesion
Keywords: Adhesin, Lectin, Nanobody, Complex, Cell Adhesion
Deposited on 2015-12-09, released 2016-01-20
The last revision prior to the SCOPe 2.07 freeze date was dated 2016-01-27, with a file datestamp of 2016-01-22.
Experiment type: XRAY
Resolution: 2.99 Å
R-factor: N/A
AEROSPACI score: 0.13 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Adhesin binding fucosylated histo-blood group antigen,Adhesin,Adhesin binding fucosylated histo-blood group antigen
    Species: Helicobacter pylori [TaxId:210]
    Gene: babA2
    Database cross-references and differences (RAF-indexed):
    • Uniprot O52269 (Start-177)
    • Uniprot Q6DSX7 (178-254)
    • Uniprot O52269 (255-460)
      • expression tag (461-464)
  • Chain 'B':
    Compound: Adhesin binding fucosylated histo-blood group antigen,Adhesin,Adhesin binding fucosylated histo-blood group antigen
    Species: Helicobacter pylori [TaxId:210]
    Gene: babA2
    Database cross-references and differences (RAF-indexed):
    • Uniprot O52269 (Start-177)
    • Uniprot Q6DSX7 (178-254)
    • Uniprot O52269 (255-460)
      • expression tag (461-463)
  • Chain 'C':
    Compound: Nanobody Nb-ER19
    Species: LAMA GLAMA [TaxId:9844]
    Gene:
    Database cross-references and differences (RAF-indexed):
    • PDB 5F93
    Domains in SCOPe 2.07: d5f93c1, d5f93c2
  • Chain 'D':
    Compound: Nanobody Nb-ER19
    Species: LAMA GLAMA [TaxId:9844]
    Gene:
    Database cross-references and differences (RAF-indexed):
    • PDB 5F93
    Domains in SCOPe 2.07: d5f93d1, d5f93d2
  • Chain 'E':
    Compound: Adhesin binding fucosylated histo-blood group antigen,Adhesin,Adhesin binding fucosylated histo-blood group antigen
    Species: Helicobacter pylori [TaxId:210]
    Gene: babA2
    Database cross-references and differences (RAF-indexed):
    • Uniprot O52269 (Start-177)
    • Uniprot Q6DSX7 (178-254)
    • Uniprot O52269 (255-460)
      • expression tag (461-463)
  • Chain 'F':
    Compound: Nanobody Nb-ER19
    Species: LAMA GLAMA [TaxId:9844]
    Gene:
    Database cross-references and differences (RAF-indexed):
    • PDB 5F93
    Domains in SCOPe 2.07: d5f93f1, d5f93f2
  • Chain 'G':
    Compound: Adhesin binding fucosylated histo-blood group antigen,Adhesin,Adhesin binding fucosylated histo-blood group antigen
    Species: Helicobacter pylori [TaxId:210]
    Gene: babA2
    Database cross-references and differences (RAF-indexed):
    • Uniprot O52269 (Start-177)
    • Uniprot Q6DSX7 (178-254)
    • Uniprot O52269 (255-460)
      • expression tag (461-463)
  • Chain 'H':
    Compound: Nanobody Nb-ER19
    Species: LAMA GLAMA [TaxId:9844]
    Gene:
    Database cross-references and differences (RAF-indexed):
    • PDB 5F93
    Domains in SCOPe 2.07: d5f93h1, d5f93h2
  • Heterogens: GLC, GAL, NAG, FUC, HOH

PDB Chain Sequences:

  • Chain 'A':
    No sequence available.

  • Chain 'B':
    No sequence available.

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >5f93C (C:)
    qvqlqesggglvqpggslrlscaasgsifsgnvmgwyrqapgklrewvaaitpqgvpnya
    dsvkgrftisrdnaknmlylqmsslkpedtalyycnrlpnyrswgqgtqvtvsshhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >5f93C (C:)
    vqlqesggglvqpggslrlscaasgsifsgnvmgwyrqapgklrewvaaitpqgvpnyad
    svkgrftisrdnaknmlylqmsslkpedtalyycnrlpnyrswgqgtqvtvssh
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >5f93D (D:)
    qvqlqesggglvqpggslrlscaasgsifsgnvmgwyrqapgklrewvaaitpqgvpnya
    dsvkgrftisrdnaknmlylqmsslkpedtalyycnrlpnyrswgqgtqvtvsshhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >5f93D (D:)
    vqlqesggglvqpggslrlscaasgsifsgnvmgwyrqapgklrewvaaitpqgvpnyad
    svkgrftisrdnaknmlylqmsslkpedtalyycnrlpnyrswgqgtqvtvssh
    

  • Chain 'E':
    No sequence available.

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >5f93F (F:)
    qvqlqesggglvqpggslrlscaasgsifsgnvmgwyrqapgklrewvaaitpqgvpnya
    dsvkgrftisrdnaknmlylqmsslkpedtalyycnrlpnyrswgqgtqvtvsshhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >5f93F (F:)
    vqlqesggglvqpggslrlscaasgsifsgnvmgwyrqapgklrewvaaitpqgvpnyad
    svkgrftisrdnaknmlylqmsslkpedtalyycnrlpnyrswgqgtqvtvssh
    

  • Chain 'G':
    No sequence available.

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >5f93H (H:)
    qvqlqesggglvqpggslrlscaasgsifsgnvmgwyrqapgklrewvaaitpqgvpnya
    dsvkgrftisrdnaknmlylqmsslkpedtalyycnrlpnyrswgqgtqvtvsshhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >5f93H (H:)
    vqlqesggglvqpggslrlscaasgsifsgnvmgwyrqapgklrewvaaitpqgvpnyad
    svkgrftisrdnaknmlylqmsslkpedtalyycnrlpnyrswgqgtqvtvssh