PDB entry 5f97

View 5f97 on RCSB PDB site
Description: Blood group antigen binding adhesin BabA of Helicobacter pylori strain A730 in complex with blood group A type 1 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 2.08 freeze date was dated 2020-07-29, with a file datestamp of 2020-06-29.
Experiment type: XRAY
Resolution: 2.62 Å
R-factor: N/A
AEROSPACI score: 0.25 (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 (461-463)
  • 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: 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 'D':
    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 'E':
    Compound: Nanbody Nb-ER19
    Species: LAMA GLAMA [TaxId:9844]
    Database cross-references and differences (RAF-indexed):
    • PDB 5F97
    Domains in SCOPe 2.08: d5f97e1, d5f97e2, d5f97e3
  • Chain 'F':
    Compound: Nanbody Nb-ER19
    Species: LAMA GLAMA [TaxId:9844]
    Database cross-references and differences (RAF-indexed):
    • PDB 5F97
    Domains in SCOPe 2.08: d5f97f1, d5f97f2, d5f97f3
  • Chain 'G':
    Compound: Nanbody Nb-ER19
    Species: LAMA GLAMA [TaxId:9844]
    Database cross-references and differences (RAF-indexed):
    • PDB 5F97
    Domains in SCOPe 2.08: d5f97g1, d5f97g2, d5f97g3
  • Chain 'H':
    Compound: Nanbody Nb-ER19
    Species: LAMA GLAMA [TaxId:9844]
    Database cross-references and differences (RAF-indexed):
    • PDB 5F97
    Domains in SCOPe 2.08: d5f97h1, d5f97h2, d5f97h3
  • Heterogens: HOH

PDB Chain Sequences:

  • Chain 'A':
    No sequence available.

  • Chain 'B':
    No sequence available.

  • Chain 'C':
    No sequence available.

  • Chain 'D':
    No sequence available.

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >5f97E (E:)
qvqlqesggglvqpggslrlscaasgsifsgnvmgwyrqapgklrewvaaitpqgvpnya
dsvkgrftisrdnaknmlylqmsslkpedtalyycnrlpnyrswgqgtqvtvsshhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >5f97E (E:)
vqlqesggglvqpggslrlscaasgsifsgnvmgwyrqapgklrewvaaitpqgvpnyad
svkgrftisrdnaknmlylqmsslkpedtalyycnrlpnyrswgqgtqvtvssh

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >5f97F (F:)
qvqlqesggglvqpggslrlscaasgsifsgnvmgwyrqapgklrewvaaitpqgvpnya
dsvkgrftisrdnaknmlylqmsslkpedtalyycnrlpnyrswgqgtqvtvsshhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >5f97F (F:)
vqlqesggglvqpggslrlscaasgsifsgnvmgwyrqapgklrewvaaitpqgvpnyad
svkgrftisrdnaknmlylqmsslkpedtalyycnrlpnyrswgqgtqvtvsshh

  • Chain 'G':
    Sequence, based on SEQRES records: (download) 
    >5f97G (G:)
qvqlqesggglvqpggslrlscaasgsifsgnvmgwyrqapgklrewvaaitpqgvpnya
dsvkgrftisrdnaknmlylqmsslkpedtalyycnrlpnyrswgqgtqvtvsshhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >5f97G (G:)
vqlqesggglvqpggslrlscaasgsifsgnvmgwyrqapgklrewvaaitpqgvpnyad
svkgrftisrdnaknmlylqmsslkpedtalyycnrlpnyrswgqgtqvtvssh

  • Chain 'H':
    Sequence, based on SEQRES records: (download) 
    >5f97H (H:)
qvqlqesggglvqpggslrlscaasgsifsgnvmgwyrqapgklrewvaaitpqgvpnya
dsvkgrftisrdnaknmlylqmsslkpedtalyycnrlpnyrswgqgtqvtvsshhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >5f97H (H:)
vqlqesggglvqpggslrlscaasgsifsgnvmgwyrqapgklrewvaaitpqgvpnyad
svkgrftisrdnaknmlylqmsslkpedtalyycnrlpnyrswgqgtqvtvss