PDB entry 5js9

View 5js9 on RCSB PDB site
Description: uncleaved prefusion optimized gp140 trimer with an engineered 8- residue hr1 turn bound to broadly neutralizing antibodies 8anc195 and pgt128
Deposited on 2016-05-07, released 2016-07-13
The last revision was dated 2020-07-29, with a file datestamp of 2020-07-09.
Experiment type: XRAY
Resolution: 6.92 Å
R-factor: N/A
AEROSPACI score: -0.05 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: broadly neutralizing antibody PGT128 heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 5JS9
  • Chain 'B':
    Compound: broadly neutralizing antibody PGT128 light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 5JS9
  • Chain 'C':
    Compound: gp120
    Species: Human immunodeficiency virus 1 [TaxId:11676]
    Database cross-references and differences (RAF-indexed):
    • PDB 5JS9
  • Chain 'D':
    Compound: gp41
    Species: HUMAN IMMUNODEFICIENCY VIRUS 1 [TaxId:11676]
    Database cross-references and differences (RAF-indexed):
    • PDB 5JS9 (Start-139)
  • Chain 'E':
    Compound: broadly neutralizing antibody 8ANC195 heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 5JS9 (0-End)
  • Chain 'F':
    Compound: broadly neutralizing antibody 8ANC195 light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 5JS9 (0-End)
  • Heterogens: NAG

PDB Chain Sequences:
This PDB entry is not classified in SCOPe 2.07, so the chain sequences below are not included in the ASTRAL sequence sets.

  • Chain 'A':
    Sequence, based on SEQRES records:
    >5js9A (A:)
    epqlqesgptlveasetlsltcavsgdstaacnsfwgwvrqppgkglewvgslshcasyw
    nrgwtyhnpslksrltlaldtpknlvflklnsvtaadtatyycarfggevlrytdwpkpa
    wvdlwgrgtlvtvssastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsga
    ltsgvhtfpavlqssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkrvepkscd
    

    Sequence, based on observed residues (ATOM records):
    >5js9A (A:)
    pqlqesgptlveasetlsltcavsgdstaacnsfwgwvrqppgkglewvgslshcasywn
    rgwtyhnpslksrltlaldtpknlvflklnsvtaadtatyycarfggevlrytdwpkpaw
    vdlwgrgtlvtvssastkgpsvfplapssggtaalgclvkdyfpepvtvswnsgaltsgv
    htfpavlqssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkrvep
    

  • Chain 'B':
    Sequence, based on SEQRES records:
    >5js9B (B:)
    qsaltqppsasgspgqsitisctgtsnnfvswyqqhagkapklviydvnkrpsgvpdrfs
    gsksgntasltvsglqtddeavyycgslvgnwdvifgggtkltvlgqpkaapsvtlfpps
    seelqankatlvclisdfypgavtvawkadsspvkagvetttpskqsnnkyaassylslt
    peqwkshrsyscqvthegstvektvaptecs
    

    Sequence, based on observed residues (ATOM records):
    >5js9B (B:)
    ltqppsasgspgqsitisctgtsnnfvswyqqhagkapklviydvnkrpsgvpdrfsgsk
    sgntasltvsglqtddeavyycgslvgnwdvifgggtkltvlgqpkaapsvtlfppssee
    lqankatlvclisdfypgavtvawkadsspvkagvetttpskqsnnkyaassylsltpeq
    wkshrsyscqvthegstvektvap
    

  • Chain 'C':
    Sequence, based on SEQRES records:
    >5js9C (C:)
    aenlwvtvyygvpvwkdaettlfcasdakayetekhnvwathacvptdpnpqeihlenvt
    eefnmwknnmveqmhtdiislwdqslkpcvkltplcvtlqctnvtaitddmrgelkncsf
    nmttelrdkkqkvyslfyrldvvqinenqgnrsnnsnkeyrlincntsaitqacpkvsfe
    pipihycapagfailkckdkkfngtgpcpsvstvqcthgikpvvstqlllngslaeeevm
    irsenitnnaknilvqfntpvqinctrpnnntrksirigpgqafyatgdiigdirqahcn
    vskatwnetlgkvvkqlrkhfgnntiirfanssggdlevtthsfncggeffycntsglfn
    stwisntsvqgsnstgsndsitlpcrikqiinmwqrigqamyappiqgvircvsnitgli
    ltrdggstnsttetfrpgggdmrdnwrselykykvvkieplgvaptrckrrvvgrrrrrr
    

    Sequence, based on observed residues (ATOM records):
    >5js9C (C:)
    nlwvtvyygvpvwkdaettlfcasdakayetekhnvwathacvptdpnpqeihlenvtee
    fnmwknnmveqmhtdiislwdqslkpcvkltplcvtlqctnvtdmrgelkncsfnmttel
    rdkkqkvyslfyrldvvqinnkeyrlincntsaitqacpkvsfepipihycapagfailk
    ckdkkfngtgpcpsvstvqcthgikpvvstqlllngslaeeevmirsenitnnaknilvq
    fntpvqinctrpnnntrksirigpgqafyatgdiigdirqahcnvskatwnetlgkvvkq
    lrkhfgnntiirfanssggdlevtthsfncggeffycntsglfnstwisntsvndsitlp
    crikqiinmwqrigqamyappiqgvircvsnitgliltrdggstnsttetfrpgggdmrd
    nwrselykykvvkieplgvaptrckrr
    

  • Chain 'D':
    Sequence, based on SEQRES records:
    >5js9D (D:)
    avgigavflgflgaagstmgaasmtltvqarnllsgnpdwlpdmtvwgikqlqarvlave
    rylrdqqllgiwgcsgklicctnvpwnsswsnrnlseiwdnmtwlqwdkeisnytqiiyg
    lleesqnqqekneqdllald
    

    Sequence, based on observed residues (ATOM records):
    >5js9D (D:)
    flgaagstmgaasmtltvqarnllsgnpdwlpdmtvwgikqlqarvlaverylrdqqllg
    iwgcsgklicctnvpwnsswsnrnlseiwdnmtwlqwdkeisnytqiiyglleesqnqqe
    kneqdllald
    

  • Chain 'E':
    Sequence, based on SEQRES records:
    >5js9E (E:)
    qihlvqsgtevkkpgssvtvsckaygvntfglyavnwvrqapgqsleyigqiwrwkssas
    hhfrgrvlisavdltgssppissleiknltsddtavyfctttstydkwsglhhdgvmafs
    swgqgtlisvsaastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgalts
    gvhtfpavlqssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepkscdkt
    

    Sequence, based on observed residues (ATOM records):
    >5js9E (E:)
    qihlvqsgtevkkpgssvtvsckaygvntfglyavnwvrqapgqsleyigqiwrwkssas
    hhfrgrvlisavdltgssppissleiknltsddtavyfctttstydkwsglhhdgvmafs
    swgqgtlisvsaastkgpsvfplapssgtaalgclvkdyfpepvtvswnsgaltsgvhtf
    pavlqssglyslssvvtvpstqtyicnvnhkpsntkvdkkvepk
    

  • Chain 'F':
    Sequence, based on SEQRES records:
    >5js9F (F:)
    diqmtqspstlsasigdtvriscrasqsitgnwvawyqqrpgkaprlliyrgaallggvp
    srfsgsaagtdftltignlqaedfgtfycqqydtypgtfgqgtkvevkrtvaapsvfifp
    psdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstl
    tlskadyekhkvyacevthqglsspvtksfnrgec
    

    Sequence, based on observed residues (ATOM records):
    >5js9F (F:)
    diqmtqspstlsasigdtvriscrasqsitgnwvawyqqrpgkaprlliyrgaallggvp
    srfsgsaagtdftltignlqaedfgtfycqqydtypgtfgqgtkvevkrtvaapsvfifp
    psdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstl
    tlskadyekhkvyacevthqglsspvtksfnr