PDB entry 5k9q

View 5k9q on RCSB PDB site
Description: Crystal structure of multidonor HV1-18-class broadly neutralizing Influenza A antibody 16.a.26 in complex with A/Hong Kong/1-4-MA21-1/1968 (H3N2) Hemagglutinin
Class: immune system
Keywords: HV1-18 (QxxV), multidonor, H5, universal influenza vaccine, IMMUNE SYSTEM
Deposited on 2016-06-01, released 2016-11-30
The last revision prior to the SCOPe 2.07 freeze date was dated 2016-11-30, with a file datestamp of 2016-11-25.
Experiment type: XRAY
Resolution: 2.5 Å
R-factor: N/A
AEROSPACI score: 0.21 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: hemagglutinin HA1
    Species: Influenza A virus [TaxId:506350]
    Gene: HA
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q91MA7 (0-319)
      • conflict (210)
      • conflict (319)
    Domains in SCOPe 2.07: d5k9qa_
  • Chain 'B':
    Compound: hemagglutinin HA2
    Species: Influenza A virus (strain A/Hong Kong/1/1968 H3N2) [TaxId:506350]
    Gene: HA
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5k9qb_
  • Chain 'C':
    Compound: hemagglutinin HA1
    Species: Influenza A virus [TaxId:506350]
    Gene: HA
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q91MA7 (0-End)
      • conflict (210)
    Domains in SCOPe 2.07: d5k9qc_
  • Chain 'D':
    Compound: hemagglutinin HA2
    Species: Influenza A virus (strain A/Hong Kong/1/1968 H3N2) [TaxId:506350]
    Gene: HA
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5k9qd_
  • Chain 'E':
    Compound: hemagglutinin HA1
    Species: Influenza A virus [TaxId:506350]
    Gene: HA
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q91MA7 (0-End)
      • conflict (210)
    Domains in SCOPe 2.07: d5k9qe_
  • Chain 'F':
    Compound: hemagglutinin HA2
    Species: Influenza A virus (strain A/Hong Kong/1/1968 H3N2) [TaxId:506350]
    Gene: HA
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5k9qf_
  • Chain 'G':
    Compound: 16.a.26 Heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 5K9Q (0-230)
  • Chain 'H':
    Compound: 16.a.26 Heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 5K9Q (0-230)
  • Chain 'I':
    Compound: 16.a.26 Light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 5K9Q (0-213)
    Domains in SCOPe 2.07: d5k9qi1, d5k9qi2
  • Chain 'J':
    Compound: 16.a.26 Heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 5K9Q (0-230)
  • Chain 'K':
    Compound: 16.a.26 Light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 5K9Q (0-213)
    Domains in SCOPe 2.07: d5k9qk1, d5k9qk2
  • Chain 'L':
    Compound: 16.a.26 Light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 5K9Q (0-213)
    Domains in SCOPe 2.07: d5k9ql1, d5k9ql2
  • Chain 'M':
    Compound: hemagglutinin HA1
    Species: Influenza A virus [TaxId:506350]
    Gene: HA
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q91MA7 (0-End)
      • conflict (210)
    Domains in SCOPe 2.07: d5k9qm_
  • Chain 'N':
    Compound: hemagglutinin HA2
    Species: Influenza A virus (strain A/Hong Kong/1/1968 H3N2) [TaxId:506350]
    Gene: HA
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5k9qn_
  • Chain 'O':
    Compound: hemagglutinin HA1
    Species: Influenza A virus [TaxId:506350]
    Gene: HA
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q91MA7 (0-End)
      • conflict (210)
    Domains in SCOPe 2.07: d5k9qo_
  • Chain 'P':
    Compound: hemagglutinin HA2
    Species: Influenza A virus (strain A/Hong Kong/1/1968 H3N2) [TaxId:506350]
    Gene: HA
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5k9qp_
  • Chain 'Q':
    Compound: hemagglutinin HA1
    Species: Influenza A virus [TaxId:506350]
    Gene: HA
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q91MA7
      • conflict (210)
    Domains in SCOPe 2.07: d5k9qq_
  • Chain 'R':
    Compound: hemagglutinin HA2
    Species: Influenza A virus (strain A/Hong Kong/1/1968 H3N2) [TaxId:506350]
    Gene: HA
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5k9qr_
  • Chain 'S':
    Compound: 16.a.26 Heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 5K9Q (0-230)
  • Chain 'T':
    Compound: 16.a.26 Light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 5K9Q (0-213)
    Domains in SCOPe 2.07: d5k9qt1, d5k9qt2
  • Chain 'U':
    Compound: 16.a.26 Heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 5K9Q (0-230)
  • Chain 'V':
    Compound: 16.a.26 Light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 5K9Q (0-213)
    Domains in SCOPe 2.07: d5k9qv1, d5k9qv2
  • Chain 'X':
    Compound: 16.a.26 Heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 5K9Q (0-230)
  • Chain 'Y':
    Compound: 16.a.26 Light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 5K9Q (0-213)
    Domains in SCOPe 2.07: d5k9qy1, d5k9qy2
  • Heterogens: NAG, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence; same for both SEQRES and ATOM records: (download)
    >5k9qA (A:)
    nstatlclghhavpngtlvktitddqievtnatelvqssstgkicnnphrildgidctli
    dallgdphcdvfqnetwdlfverskafsncypydvpdyaslrslvassgtlefitegftw
    tgvtqnggsnackrgpgsgffsrlnwltksgstypvlnvtmpnndnfdklyiwgvhhpst
    nqeqtslyvqasgrvtvstrrsqqtiipniesrpwvrglssrisiywtivkpgdvlvins
    ngnliaprgyfkmrtgkssimrsdapidtcisecitpngsipndkpfqnvnkitygacpk
    yvkqntlklatgmrnvpeka
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >5k9qB (B:)
    fgaiagfiengwegmidgwygfrhqnsegtgqaadlkstqaaidqingklnrviektnek
    fhqiekefsevegriqdlekyvedtkidlwsynaellvalenqhtidltdsemnklfekt
    rrqlrenaedmgngcfkiyhkcdnaciesirngtydhdvyrdealnnrfq
    

    Sequence, based on observed residues (ATOM records): (download)
    >5k9qB (B:)
    gaiagfiengwegmidgwygfrhqnsegtgqaadlkstqaaidqingklnrviektnekf
    hqiekefsevegriqdlekyvedtkidlwsynaellvalenqhtidltdsemnklfektr
    rqlrenaedmgngcfkiyhkcdnaciesirngtydhdvyrdealnnrf
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >5k9qC (C:)
    nstatlclghhavpngtlvktitddqievtnatelvqssstgkicnnphrildgidctli
    dallgdphcdvfqnetwdlfverskafsncypydvpdyaslrslvassgtlefitegftw
    tgvtqnggsnackrgpgsgffsrlnwltksgstypvlnvtmpnndnfdklyiwgvhhpst
    nqeqtslyvqasgrvtvstrrsqqtiipniesrpwvrglssrisiywtivkpgdvlvins
    ngnliaprgyfkmrtgkssimrsdapidtcisecitpngsipndkpfqnvnkitygacpk
    yvkqntlklatgmrnvpeka
    

    Sequence, based on observed residues (ATOM records): (download)
    >5k9qC (C:)
    nstatlclghhavpngtlvktitddqievtnatelvqssstgkicnnphrildgidctli
    dallgdphcdvfqnetwdlfverskafsncypydvpdyaslrslvassgtlefitegftw
    tgvtqnggsnackrgpgsgffsrlnwltksgstypvlnvtmpnndnfdklyiwgvhhpst
    nqeqtslyvqasgrvtvstrrsqqtiipniesrpwvrglssrisiywtivkpgdvlvins
    ngnliaprgyfkmrtgkssimrsdapidtcisecitpngsipndkpfqnvnkitygacpk
    yvkqntlklatgmrnvpek
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >5k9qD (D:)
    fgaiagfiengwegmidgwygfrhqnsegtgqaadlkstqaaidqingklnrviektnek
    fhqiekefsevegriqdlekyvedtkidlwsynaellvalenqhtidltdsemnklfekt
    rrqlrenaedmgngcfkiyhkcdnaciesirngtydhdvyrdealnnrfq
    

    Sequence, based on observed residues (ATOM records): (download)
    >5k9qD (D:)
    fgaiagfiengwegmidgwygfrhqnsegtgqaadlkstqaaidqingklnrviektnek
    fhqiekefsevegriqdlekyvedtkidlwsynaellvalenqhtidltdsemnklfekt
    rrqlrenaedmgngcfkiyhkcdnaciesirngtydhdvyrdealnnrf
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >5k9qE (E:)
    nstatlclghhavpngtlvktitddqievtnatelvqssstgkicnnphrildgidctli
    dallgdphcdvfqnetwdlfverskafsncypydvpdyaslrslvassgtlefitegftw
    tgvtqnggsnackrgpgsgffsrlnwltksgstypvlnvtmpnndnfdklyiwgvhhpst
    nqeqtslyvqasgrvtvstrrsqqtiipniesrpwvrglssrisiywtivkpgdvlvins
    ngnliaprgyfkmrtgkssimrsdapidtcisecitpngsipndkpfqnvnkitygacpk
    yvkqntlklatgmrnvpeka
    

    Sequence, based on observed residues (ATOM records): (download)
    >5k9qE (E:)
    nstatlclghhavpngtlvktitddqievtnatelvqssstgkicnnphrildgidctli
    dallgdphcdvfqnetwdlfverskafsncypydvpdyaslrslvassgtlefitegftw
    tgvtqnggsnackrgpgsgffsrlnwltksgstypvlnvtmpnndnfdklyiwgvhhpst
    nqeqtslyvqasgrvtvstrrsqqtiipniesrpwvrglssrisiywtivkpgdvlvins
    ngnliaprgyfkmrtgkssimrsdapidtcisecitpngsipndkpfqnvnkitygacpk
    yvkqntlklatgmrnvpe
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >5k9qF (F:)
    fgaiagfiengwegmidgwygfrhqnsegtgqaadlkstqaaidqingklnrviektnek
    fhqiekefsevegriqdlekyvedtkidlwsynaellvalenqhtidltdsemnklfekt
    rrqlrenaedmgngcfkiyhkcdnaciesirngtydhdvyrdealnnrfq
    

    Sequence, based on observed residues (ATOM records): (download)
    >5k9qF (F:)
    aiagfiengwegmidgwygfrhqnsegtgqaadlkstqaaidqingklnrviektnekfh
    qiekefsevegriqdlekyvedtkidlwsynaellvalenqhtidltdsemnklfektrr
    qlrenaedmgngcfkiyhkcdnaciesirngtydhdvyrdealnnrfq
    

  • Chain 'G':
    No sequence available.

  • Chain 'H':
    No sequence available.

  • Chain 'I':
    Sequence; same for both SEQRES and ATOM records: (download)
    >5k9qI (I:)
    diqmtqspvslsasvgdrvtitcrasqsigkflnwyqqkpgrapklliyyasnletggps
    rfsgrgsetefsltisslqpedfatyycqqsnnvphtfgqgtkleikrtvaapsvfifpp
    sdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstlt
    lskadyekhkvyacevthqglsspvtksfnrgec
    

  • Chain 'J':
    No sequence available.

  • Chain 'K':
    Sequence; same for both SEQRES and ATOM records: (download)
    >5k9qK (K:)
    diqmtqspvslsasvgdrvtitcrasqsigkflnwyqqkpgrapklliyyasnletggps
    rfsgrgsetefsltisslqpedfatyycqqsnnvphtfgqgtkleikrtvaapsvfifpp
    sdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstlt
    lskadyekhkvyacevthqglsspvtksfnrgec
    

  • Chain 'L':
    Sequence; same for both SEQRES and ATOM records: (download)
    >5k9qL (L:)
    diqmtqspvslsasvgdrvtitcrasqsigkflnwyqqkpgrapklliyyasnletggps
    rfsgrgsetefsltisslqpedfatyycqqsnnvphtfgqgtkleikrtvaapsvfifpp
    sdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstlt
    lskadyekhkvyacevthqglsspvtksfnrgec
    

  • Chain 'M':
    Sequence, based on SEQRES records: (download)
    >5k9qM (M:)
    nstatlclghhavpngtlvktitddqievtnatelvqssstgkicnnphrildgidctli
    dallgdphcdvfqnetwdlfverskafsncypydvpdyaslrslvassgtlefitegftw
    tgvtqnggsnackrgpgsgffsrlnwltksgstypvlnvtmpnndnfdklyiwgvhhpst
    nqeqtslyvqasgrvtvstrrsqqtiipniesrpwvrglssrisiywtivkpgdvlvins
    ngnliaprgyfkmrtgkssimrsdapidtcisecitpngsipndkpfqnvnkitygacpk
    yvkqntlklatgmrnvpeka
    

    Sequence, based on observed residues (ATOM records): (download)
    >5k9qM (M:)
    nstatlclghhavpngtlvktitddqievtnatelvqssstgkicnnphrildgidctli
    dallgdphcdvfqnetwdlfverskafsncypydvpdyaslrslvassgtlefitegftw
    tgvtqnggsnackrgpgsgffsrlnwltksgstypvlnvtmpnndnfdklyiwgvhhpst
    nqeqtslyvqasgrvtvstrrsqqtiipniesrpwvrglssrisiywtivkpgdvlvins
    ngnliaprgyfkmrtgkssimrsdapidtcisecitpngsipndkpfqnvnkitygacpk
    yvkqntlklatgmrnvpe
    

  • Chain 'N':
    Sequence, based on SEQRES records: (download)
    >5k9qN (N:)
    fgaiagfiengwegmidgwygfrhqnsegtgqaadlkstqaaidqingklnrviektnek
    fhqiekefsevegriqdlekyvedtkidlwsynaellvalenqhtidltdsemnklfekt
    rrqlrenaedmgngcfkiyhkcdnaciesirngtydhdvyrdealnnrfq
    

    Sequence, based on observed residues (ATOM records): (download)
    >5k9qN (N:)
    gaiagfiengwegmidgwygfrhqnsegtgqaadlkstqaaidqingklnrviektnekf
    hqiekefsevegriqdlekyvedtkidlwsynaellvalenqhtidltdsemnklfektr
    rqlrenaedmgngcfkiyhkcdnaciesirngtydhdvyrdealnnrfq
    

  • Chain 'O':
    Sequence, based on SEQRES records: (download)
    >5k9qO (O:)
    nstatlclghhavpngtlvktitddqievtnatelvqssstgkicnnphrildgidctli
    dallgdphcdvfqnetwdlfverskafsncypydvpdyaslrslvassgtlefitegftw
    tgvtqnggsnackrgpgsgffsrlnwltksgstypvlnvtmpnndnfdklyiwgvhhpst
    nqeqtslyvqasgrvtvstrrsqqtiipniesrpwvrglssrisiywtivkpgdvlvins
    ngnliaprgyfkmrtgkssimrsdapidtcisecitpngsipndkpfqnvnkitygacpk
    yvkqntlklatgmrnvpeka
    

    Sequence, based on observed residues (ATOM records): (download)
    >5k9qO (O:)
    nstatlclghhavpngtlvktitddqievtnatelvqssstgkicnnphrildgidctli
    dallgdphcdvfqnetwdlfverskafsncypydvpdyaslrslvassgtlefitegftw
    tgvtqnggsnackrgpgsgffsrlnwltksgstypvlnvtmpnndnfdklyiwgvhhpst
    nqeqtslyvqasgrvtvstrrsqqtiipniesrpwvrglssrisiywtivkpgdvlvins
    ngnliaprgyfkmrtgkssimrsdapidtcisecitpngsipndkpfqnvnkitygacpk
    yvkqntlklatgmrnvpe
    

  • Chain 'P':
    Sequence, based on SEQRES records: (download)
    >5k9qP (P:)
    fgaiagfiengwegmidgwygfrhqnsegtgqaadlkstqaaidqingklnrviektnek
    fhqiekefsevegriqdlekyvedtkidlwsynaellvalenqhtidltdsemnklfekt
    rrqlrenaedmgngcfkiyhkcdnaciesirngtydhdvyrdealnnrfq
    

    Sequence, based on observed residues (ATOM records): (download)
    >5k9qP (P:)
    fiengwegmidgwygfrhqnsegtgqaadlkstqaaidqingklnrviektnekfhqiek
    efsevegriqdlekyvedtkidlwsynaellvalenqhtidltdsemnklfektrrqlre
    naedmgngcfkiyhkcdnaciesirngtydhdvyrdealnnrf
    

  • Chain 'Q':
    Sequence, based on SEQRES records: (download)
    >5k9qQ (Q:)
    nstatlclghhavpngtlvktitddqievtnatelvqssstgkicnnphrildgidctli
    dallgdphcdvfqnetwdlfverskafsncypydvpdyaslrslvassgtlefitegftw
    tgvtqnggsnackrgpgsgffsrlnwltksgstypvlnvtmpnndnfdklyiwgvhhpst
    nqeqtslyvqasgrvtvstrrsqqtiipniesrpwvrglssrisiywtivkpgdvlvins
    ngnliaprgyfkmrtgkssimrsdapidtcisecitpngsipndkpfqnvnkitygacpk
    yvkqntlklatgmrnvpeka
    

    Sequence, based on observed residues (ATOM records): (download)
    >5k9qQ (Q:)
    statlclghhavpngtlvktitddqievtnatelvqssstgkicnnphrildgidctlid
    allgdphcdvfqnetwdlfverskafsncypydvpdyaslrslvassgtlefitegftwt
    gvtqnggsnackrgpgsgffsrlnwltksgstypvlnvtmpnndnfdklyiwgvhhpstn
    qeqtslyvqasgrvtvstrrsqqtiipniesrpwvrglssrisiywtivkpgdvlvinsn
    gnliaprgyfkmrtgkssimrsdapidtcisecitpngsipndkpfqnvnkitygacpky
    vkqntlklatgmrnvpek
    

  • Chain 'R':
    Sequence, based on SEQRES records: (download)
    >5k9qR (R:)
    fgaiagfiengwegmidgwygfrhqnsegtgqaadlkstqaaidqingklnrviektnek
    fhqiekefsevegriqdlekyvedtkidlwsynaellvalenqhtidltdsemnklfekt
    rrqlrenaedmgngcfkiyhkcdnaciesirngtydhdvyrdealnnrfq
    

    Sequence, based on observed residues (ATOM records): (download)
    >5k9qR (R:)
    aiagfiengwegmidgwygfrhqnsegtgqaadlkstqaaidqingklnrviektnekfh
    qiekefsevegriqdlekyvedtkidlwsynaellvalenqhtidltdsemnklfektrr
    qlrenaedmgngcfkiyhkcdnaciesirngtydhdvyrdealnnrf
    

  • Chain 'S':
    No sequence available.

  • Chain 'T':
    Sequence; same for both SEQRES and ATOM records: (download)
    >5k9qT (T:)
    diqmtqspvslsasvgdrvtitcrasqsigkflnwyqqkpgrapklliyyasnletggps
    rfsgrgsetefsltisslqpedfatyycqqsnnvphtfgqgtkleikrtvaapsvfifpp
    sdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstlt
    lskadyekhkvyacevthqglsspvtksfnrgec
    

  • Chain 'U':
    No sequence available.

  • Chain 'V':
    Sequence; same for both SEQRES and ATOM records: (download)
    >5k9qV (V:)
    diqmtqspvslsasvgdrvtitcrasqsigkflnwyqqkpgrapklliyyasnletggps
    rfsgrgsetefsltisslqpedfatyycqqsnnvphtfgqgtkleikrtvaapsvfifpp
    sdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstlt
    lskadyekhkvyacevthqglsspvtksfnrgec
    

  • Chain 'X':
    No sequence available.

  • Chain 'Y':
    Sequence; same for both SEQRES and ATOM records: (download)
    >5k9qY (Y:)
    diqmtqspvslsasvgdrvtitcrasqsigkflnwyqqkpgrapklliyyasnletggps
    rfsgrgsetefsltisslqpedfatyycqqsnnvphtfgqgtkleikrtvaapsvfifpp
    sdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstlt
    lskadyekhkvyacevthqglsspvtksfnrgec