PDB entry 3gbm

View 3gbm on RCSB PDB site
Description: Crystal Structure of Fab CR6261 in Complex with a H5N1 influenza virus hemagglutinin.
Class: viral protein / immune system
Keywords: hemagglutinin, Fab, neutralizing antibodies, antibody, avian flu, Envelope protein, Fusion protein, viral protein - immune system COMPLEX
Deposited on 2009-02-20, released 2009-03-10
The last revision prior to the SCOPe 2.07 freeze date was dated 2011-07-13, with a file datestamp of 2011-05-08.
Experiment type: XRAY
Resolution: 2.7 Å
R-factor: 0.206
AEROSPACI score: 0.28 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Hemagglutinin
    Species: Influenza A virus (A/Viet Nam/1203/2004(H5N1)) [TaxId:284218]
    Gene: HA, Hemagglutinin (HA)
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q6DQ33 (4-End)
      • expression tag (1-3)
    Domains in SCOPe 2.07: d3gbma1, d3gbma2
  • Chain 'B':
    Compound: Hemagglutinin
    Species: Influenza A virus (A/Viet Nam/1203/2004(H5N1)) [TaxId:284218]
    Gene: HA, Hemagglutinin (HA)
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q6DQ33 (0-173)
      • expression tag (174-176)
    Domains in SCOPe 2.07: d3gbmb1, d3gbmb2
  • Chain 'C':
    Compound: Hemagglutinin
    Species: Influenza A virus (A/Viet Nam/1203/2004(H5N1)) [TaxId:284218]
    Gene: HA, Hemagglutinin (HA)
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q6DQ33 (4-End)
      • expression tag (2-3)
    Domains in SCOPe 2.07: d3gbmc1, d3gbmc2
  • Chain 'D':
    Compound: Hemagglutinin
    Species: Influenza A virus (A/Viet Nam/1203/2004(H5N1)) [TaxId:284218]
    Gene: HA, Hemagglutinin (HA)
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3gbmd_
  • Chain 'H':
    Compound: antibody (Fab)
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 3GBM (0-End)
  • Chain 'I':
    Compound: antibody (Fab)
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 3GBM (0-End)
  • Chain 'L':
    Compound: antibody (Fab)
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 3GBM
    Domains in SCOPe 2.07: d3gbml1, d3gbml2
  • Chain 'M':
    Compound: antibody (Fab)
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 3GBM
    Domains in SCOPe 2.07: d3gbmm1, d3gbmm2
  • Heterogens: NAG, BMA, EDO, GOL, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >3gbmA (A:)
    adpgdqicigyhannsteqvdtimeknvtvthaqdilekkhngklcdldgvkplilrdcs
    vagwllgnpmcdefinvpewsyivekanpvndlcypgdfndyeelkhllsrinhfekiqi
    ipksswssheaslgvssacpyqgkssffrnvvwlikknstyptikrsynntnqedllvlw
    gihhpndaaeqtklyqnpttyisvgtstlnqrlvpriatrskvngqsgrmeffwtilkpn
    dainfesngnfiapeyaykivkkgdstimkseleygncntkcqtpmgainssmpfhnihp
    ltigecpkyvksnrlvlatglrnspqrerrrkkr
    

    Sequence, based on observed residues (ATOM records): (download)
    >3gbmA (A:)
    dpgdqicigyhannsteqvdtimeknvtvthaqdilekkhngklcdldgvkplilrdcsv
    agwllgnpmcdefinvpewsyivekanpvndlcypgdfndyeelkhllsrinhfekiqii
    pksswssheaslgvssacpyqgkssffrnvvwlikknstyptikrsynntnqedllvlwg
    ihhpndaaeqtklyqnpttyisvgtstlnqrlvpriatrskvngqsgrmeffwtilkpnd
    ainfesngnfiapeyaykivkkgdstimkseleygncntkcqtpmgainssmpfhnihpl
    tigecpkyvksnrlvlatglrnsp
    

  • Chain 'B':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3gbmB (B:)
    glfgaiagfieggwqgmvdgwygyhhsneqgsgyaadkestqkaidgvtnkvnsiidkmn
    tqfeavgrefnnlerrienlnkkmedgfldvwtynaellvlmenertldfhdsnvknlyd
    kvrlqlrdnakelgngcfefyhkcdnecmesvrngtydypqyseearlkreeissgr
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >3gbmC (C:)
    adpgdqicigyhannsteqvdtimeknvtvthaqdilekkhngklcdldgvkplilrdcs
    vagwllgnpmcdefinvpewsyivekanpvndlcypgdfndyeelkhllsrinhfekiqi
    ipksswssheaslgvssacpyqgkssffrnvvwlikknstyptikrsynntnqedllvlw
    gihhpndaaeqtklyqnpttyisvgtstlnqrlvpriatrskvngqsgrmeffwtilkpn
    dainfesngnfiapeyaykivkkgdstimkseleygncntkcqtpmgainssmpfhnihp
    ltigecpkyvksnrlvlatglrnspqrerrrkkr
    

    Sequence, based on observed residues (ATOM records): (download)
    >3gbmC (C:)
    pgdqicigyhannsteqvdtimeknvtvthaqdilekkhngklcdldgvkplilrdcsva
    gwllgnpmcdefinvpewsyivekanpvndlcypgdfndyeelkhllsrinhfekiqiip
    ksswssheaslgvssacpyqgkssffrnvvwlikknstyptikrsynntnqedllvlwgi
    hhpndaaeqtklyqnpttyisvgtstlnqrlvpriatrskvngqsgrmeffwtilkpnda
    infesngnfiapeyaykivkkgdstimkseleygncntkcqtpmgainssmpfhnihplt
    igecpkyvksnrlvlatglrnsp
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >3gbmD (D:)
    glfgaiagfieggwqgmvdgwygyhhsneqgsgyaadkestqkaidgvtnkvnsiidkmn
    tqfeavgrefnnlerrienlnkkmedgfldvwtynaellvlmenertldfhdsnvknlyd
    kvrlqlrdnakelgngcfefyhkcdnecmesvrngtydypqyseearlkreeissgr
    

    Sequence, based on observed residues (ATOM records): (download)
    >3gbmD (D:)
    glfgaiagfieggwqgmvdgwygyhhsneqgsgyaadkestqkaidgvtnkvnsiidkmn
    tqfeavgrefnnlerrienlnkkmedgfldvwtynaellvlmenertldfhdsnvknlyd
    kvrlqlrdnakelgngcfefyhkcdnecmesvrngtydypqyseearlkreei
    

  • Chain 'H':
    No sequence available.

  • Chain 'I':
    No sequence available.

  • Chain 'L':
    Sequence, based on SEQRES records: (download)
    >3gbmL (L:)
    qsvltqppsvsaapgqkvtiscsgsssnigndyvswyqqlpgtapklliydnnkrpsgip
    drfsgsksgtsatlgitglqtgdeanyycatwdrrptayvvfgggtkltvlgaaagqpka
    apsvtlfppsseelqankatlvclisdfypgavtvawkadsspvkagvetttpskqsnnk
    yaassylsltpeqwkshrsyscqvthegstvektvaptecs
    

    Sequence, based on observed residues (ATOM records): (download)
    >3gbmL (L:)
    vltqppsvsaapgqkvtiscsgsssnigndyvswyqqlpgtapklliydnnkrpsgipdr
    fsgsksgtsatlgitglqtgdeanyycatwdrtayvvfgggtkltqpkaapsvtlfppss
    eelqankatlvclisdfypgavtvawkadsspvkagvetttpskqsnnkyaassylsltp
    eqwkshrsyscqvthegstvektvapte
    

  • Chain 'M':
    Sequence, based on SEQRES records: (download)
    >3gbmM (M:)
    qsvltqppsvsaapgqkvtiscsgsssnigndyvswyqqlpgtapklliydnnkrpsgip
    drfsgsksgtsatlgitglqtgdeanyycatwdrrptayvvfgggtkltvlgaaagqpka
    apsvtlfppsseelqankatlvclisdfypgavtvawkadsspvkagvetttpskqsnnk
    yaassylsltpeqwkshrsyscqvthegstvektvaptecs
    

    Sequence, based on observed residues (ATOM records): (download)
    >3gbmM (M:)
    vltqppsvsaapgqkvtiscsgsssnigndyvswyqqlpgtapklliydnnkrpsgipdr
    fsgsksgtsatlgitglqtgdeanyycatwdrtayvvfgggtkltvlapsvtlfppssee
    lqankatlvclisdfypgavtvawkaagvetttpskqsnnkyaassylsltpeqwkshrs
    yscqvthestvektvap