PDB entry 7k8y

View 7k8y on RCSB PDB site
Description: structure of the sars-cov-2 s 2p trimer in complex with the human neutralizing antibody fab fragment, c121 (state 2)
Deposited on 2020-09-27, released 2020-10-21
The last revision was dated 2021-01-13, with a file datestamp of 2021-01-08.
Experiment type: EM
Resolution: 4.4 Å
R-factor: N/A
AEROSPACI score: 0.09 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'B':
    Compound: Spike glycoprotein
    Species: Severe acute respiratory syndrome coronavirus 2 [TaxId:2697049]
    Gene: S, 2
    Database cross-references and differences (RAF-indexed):
    • Uniprot P0DTC2
      • conflict (985-986)
  • Chain 'D':
    Compound: Spike glycoprotein
    Species: Severe acute respiratory syndrome coronavirus 2 [TaxId:2697049]
    Gene: S, 2
    Database cross-references and differences (RAF-indexed):
    • Uniprot P0DTC2
      • conflict (985-986)
  • Chain 'E':
    Compound: Spike glycoprotein
    Species: Severe acute respiratory syndrome coronavirus 2 [TaxId:2697049]
    Gene: S, 2
    Database cross-references and differences (RAF-indexed):
    • Uniprot P0DTC2
      • conflict (985-986)
  • Chain 'G':
    Compound: C121 Fab Heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7K8Y (0-End)
  • Chain 'I':
    Compound: C121 Fab Light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7K8Y
  • Heterogens: NAG

PDB Chain Sequences:
This PDB entry is not classified in SCOPe 2.08, so the chain sequences below are not included in the ASTRAL sequence sets.

  • Chain 'B':
    Sequence, based on SEQRES records:
    >7k8yB (B:)
    mfvflvllplvssqcvnlttrtqlppaytnsftrgvyypdkvfrssvlhstqdlflpffs
    nvtwfhaihvsgtngtkrfdnpvlpfndgvyfasteksniirgwifgttldsktqslliv
    nnatnvvikvcefqfcndpflgvyyhknnkswmesefrvyssannctfeyvsqpflmdle
    gkqgnfknlrefvfknidgyfkiyskhtpinlvrdlpqgfsaleplvdlpiginitrfqt
    llalhrsyltpgdsssgwtagaaayyvgylqprtfllkynengtitdavdcaldplsetk
    ctlksftvekgiyqtsnfrvqptesivrfpnitnlcpfgevfnatrfasvyawnrkrisn
    cvadysvlynsasfstfkcygvsptklndlcftnvyadsfvirgdevrqiapgqtgkiad
    ynyklpddftgcviawnsnnldskvggnynylyrlfrksnlkpferdisteiyqagstpc
    ngvegfncyfplqsygfqptngvgyqpyrvvvlsfellhapatvcgpkkstnlvknkcvn
    fnfngltgtgvltesnkkflpfqqfgrdiadttdavrdpqtleilditpcsfggvsvitp
    gtntsnqvavlyqdvnctevpvaihadqltptwrvystgsnvfqtragcligaehvnnsy
    ecdipigagicasyqtqtnsprrarsvasqsiiaytmslgaensvaysnnsiaiptnfti
    svtteilpvsmtktsvdctmyicgdstecsnlllqygsfctqlnraltgiaveqdkntqe
    vfaqvkqiyktppikdfggfnfsqilpdpskpskrsfiedllfnkvtladagfikqygdc
    lgdiaardlicaqkfngltvlpplltdemiaqytsallagtitsgwtfgagaalqipfam
    qmayrfngigvtqnvlyenqklianqfnsaigkiqdslsstasalgklqdvvnqnaqaln
    tlvkqlssnfgaissvlndilsrldppeaevqidrlitgrlqslqtyvtqqliraaeira
    sanlaatkmsecvlgqskrvdfcgkgyhlmsfpqsaphgvvflhvtyvpaqeknfttapa
    ichdgkahfpregvfvsngthwfvtqrnfyepqiittdntfvsgncdvvigivnntvydp
    lqpeldsfkeeldkyfknhtspdvdlgdisginasvvniqkeidrlnevaknlneslidl
    qelgkyeqyikwpsgrlvprgspgsgyipeaprdgqayvrkdgewvllstflghhhhhh
    

    Sequence, based on observed residues (ATOM records):
    >7k8yB (B:)
    aytnsftrgvyypdkvfrssvlhstqdlflpffsnvtwfhaihdnpvlpfndgvyfaste
    ksniirgwifgttldsktqsllivnnatnvvikvcefqfcndpflgvnctfeyvsfknlr
    efvfknidgyfkiyskhtpinlvrdlpqgfsaleplvdlpiginitrfqtllalhaayyv
    gylqprtfllkynengtitdavdcaldplsetkctlksftvekgiyqtsnfrvqptesiv
    rfpnitnlcpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygvsptkl
    ndlcftnvyadsfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnldskvgg
    nynylyrlfrksnlkpferdisteiyqagstpcngvegfncyfplqsygfqptngvgyqp
    yrvvvlsfellhapatvcgpkkstnlvknkcvnfnfngltgtgvltesnkkflpfqqfgr
    diadttdavrdpqtleilditpcsfggvsvitpgtntsnqvavlyqdvnctevnvfqtra
    gcligaehvnnsyecdipigagicasyqtsqsiiaytmslgaensvaysnnsiaiptnft
    isvtteilpvsmtktsvdctmyicgdstecsnlllqygsfctqlnraltgiaveqdkntq
    evfaqvkqiyktppikdfggfnfsqilpdpskpskrsfiedllfnkvtkfngltvlppll
    tdemiaqytsallagtitsgwtfgagaalqipfamqmayrfngigvtqnvlyenqklian
    qfnsaigkiqdslsstasalgklqdvvnqnaqalntlvkqlssnfgaissvlndilsrld
    ppeaevqidrlitgrlqslqtyvtqqliraaeirasanlaatkmsecvlgqskrvdfcgk
    gyhlmsfpqsaphgvvflhvtyvpaqeknfttapaichdgkahfpregvfvsngthwfvt
    qrnfyepqiittdntfvsgncdvvigivnntvydplqpelds
    

  • Chain 'D':
    Sequence, based on SEQRES records:
    >7k8yD (D:)
    mfvflvllplvssqcvnlttrtqlppaytnsftrgvyypdkvfrssvlhstqdlflpffs
    nvtwfhaihvsgtngtkrfdnpvlpfndgvyfasteksniirgwifgttldsktqslliv
    nnatnvvikvcefqfcndpflgvyyhknnkswmesefrvyssannctfeyvsqpflmdle
    gkqgnfknlrefvfknidgyfkiyskhtpinlvrdlpqgfsaleplvdlpiginitrfqt
    llalhrsyltpgdsssgwtagaaayyvgylqprtfllkynengtitdavdcaldplsetk
    ctlksftvekgiyqtsnfrvqptesivrfpnitnlcpfgevfnatrfasvyawnrkrisn
    cvadysvlynsasfstfkcygvsptklndlcftnvyadsfvirgdevrqiapgqtgkiad
    ynyklpddftgcviawnsnnldskvggnynylyrlfrksnlkpferdisteiyqagstpc
    ngvegfncyfplqsygfqptngvgyqpyrvvvlsfellhapatvcgpkkstnlvknkcvn
    fnfngltgtgvltesnkkflpfqqfgrdiadttdavrdpqtleilditpcsfggvsvitp
    gtntsnqvavlyqdvnctevpvaihadqltptwrvystgsnvfqtragcligaehvnnsy
    ecdipigagicasyqtqtnsprrarsvasqsiiaytmslgaensvaysnnsiaiptnfti
    svtteilpvsmtktsvdctmyicgdstecsnlllqygsfctqlnraltgiaveqdkntqe
    vfaqvkqiyktppikdfggfnfsqilpdpskpskrsfiedllfnkvtladagfikqygdc
    lgdiaardlicaqkfngltvlpplltdemiaqytsallagtitsgwtfgagaalqipfam
    qmayrfngigvtqnvlyenqklianqfnsaigkiqdslsstasalgklqdvvnqnaqaln
    tlvkqlssnfgaissvlndilsrldppeaevqidrlitgrlqslqtyvtqqliraaeira
    sanlaatkmsecvlgqskrvdfcgkgyhlmsfpqsaphgvvflhvtyvpaqeknfttapa
    ichdgkahfpregvfvsngthwfvtqrnfyepqiittdntfvsgncdvvigivnntvydp
    lqpeldsfkeeldkyfknhtspdvdlgdisginasvvniqkeidrlnevaknlneslidl
    qelgkyeqyikwpsgrlvprgspgsgyipeaprdgqayvrkdgewvllstflghhhhhh
    

    Sequence, based on observed residues (ATOM records):
    >7k8yD (D:)
    aytnsftrgvyypdkvfrssvlhstqdlflpffsnvtwfhaihdnpvlpfndgvyfaste
    ksniirgwifgttldsktqsllivnnatnvvikvcefqfcndpflgvnctfeyvsfknlr
    efvfknidgyfkiyskhtpinlvrdlpqgfsaleplvdlpiginitrfqtllalhaayyv
    gylqprtfllkynengtitdavdcaldplsetkctlksftvekgiyqtsnfrvqptesiv
    rfpnitnlcpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygvsptkl
    ndlcftnvyadsfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnldskvgg
    nynylyrlfrksnlkpferdisteiyqagstpcngvegfncyfplqsygfqptngvgyqp
    yrvvvlsfellhapatvcgpkkstnlvknkcvnfnfngltgtgvltesnkkflpfqqfgr
    diadttdavrdpqtleilditpcsfggvsvitpgtntsnqvavlyqdvnctevnvfqtra
    gcligaehvnnsyecdipigagicasyqtsqsiiaytmslgaensvaysnnsiaiptnft
    isvtteilpvsmtktsvdctmyicgdstecsnlllqygsfctqlnraltgiaveqdkntq
    evfaqvkqiyktppikdfggfnfsqilpdpskpskrsfiedllfnkvtkfngltvlppll
    tdemiaqytsallagtitsgwtfgagaalqipfamqmayrfngigvtqnvlyenqklian
    qfnsaigkiqdslsstasalgklqdvvnqnaqalntlvkqlssnfgaissvlndilsrld
    ppeaevqidrlitgrlqslqtyvtqqliraaeirasanlaatkmsecvlgqskrvdfcgk
    gyhlmsfpqsaphgvvflhvtyvpaqeknfttapaichdgkahfpregvfvsngthwfvt
    qrnfyepqiittdntfvsgncdvvigivnntvydplqpelds
    

  • Chain 'E':
    Sequence, based on SEQRES records:
    >7k8yE (E:)
    mfvflvllplvssqcvnlttrtqlppaytnsftrgvyypdkvfrssvlhstqdlflpffs
    nvtwfhaihvsgtngtkrfdnpvlpfndgvyfasteksniirgwifgttldsktqslliv
    nnatnvvikvcefqfcndpflgvyyhknnkswmesefrvyssannctfeyvsqpflmdle
    gkqgnfknlrefvfknidgyfkiyskhtpinlvrdlpqgfsaleplvdlpiginitrfqt
    llalhrsyltpgdsssgwtagaaayyvgylqprtfllkynengtitdavdcaldplsetk
    ctlksftvekgiyqtsnfrvqptesivrfpnitnlcpfgevfnatrfasvyawnrkrisn
    cvadysvlynsasfstfkcygvsptklndlcftnvyadsfvirgdevrqiapgqtgkiad
    ynyklpddftgcviawnsnnldskvggnynylyrlfrksnlkpferdisteiyqagstpc
    ngvegfncyfplqsygfqptngvgyqpyrvvvlsfellhapatvcgpkkstnlvknkcvn
    fnfngltgtgvltesnkkflpfqqfgrdiadttdavrdpqtleilditpcsfggvsvitp
    gtntsnqvavlyqdvnctevpvaihadqltptwrvystgsnvfqtragcligaehvnnsy
    ecdipigagicasyqtqtnsprrarsvasqsiiaytmslgaensvaysnnsiaiptnfti
    svtteilpvsmtktsvdctmyicgdstecsnlllqygsfctqlnraltgiaveqdkntqe
    vfaqvkqiyktppikdfggfnfsqilpdpskpskrsfiedllfnkvtladagfikqygdc
    lgdiaardlicaqkfngltvlpplltdemiaqytsallagtitsgwtfgagaalqipfam
    qmayrfngigvtqnvlyenqklianqfnsaigkiqdslsstasalgklqdvvnqnaqaln
    tlvkqlssnfgaissvlndilsrldppeaevqidrlitgrlqslqtyvtqqliraaeira
    sanlaatkmsecvlgqskrvdfcgkgyhlmsfpqsaphgvvflhvtyvpaqeknfttapa
    ichdgkahfpregvfvsngthwfvtqrnfyepqiittdntfvsgncdvvigivnntvydp
    lqpeldsfkeeldkyfknhtspdvdlgdisginasvvniqkeidrlnevaknlneslidl
    qelgkyeqyikwpsgrlvprgspgsgyipeaprdgqayvrkdgewvllstflghhhhhh
    

    Sequence, based on observed residues (ATOM records):
    >7k8yE (E:)
    aytnsftrgvyypdkvfrssvlhstqdlflpffsnvtwfhaihdnpvlpfndgvyfaste
    ksniirgwifgttldsktqsllivnnatnvvikvcefqfcndpflgvnctfeyvsfknlr
    efvfknidgyfkiyskhtpinlvrdlpqgfsaleplvdlpiginitrfqtllalhaayyv
    gylqprtfllkynengtitdavdcaldplsetkctlksftvekgiyqtsnfrvqptesiv
    rfpnitnlcpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygvsptkl
    ndlcftnvyadsfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnldskvgg
    nynylyrlfrksnlkpferdisteiyqagstpcngvegfncyfplqsygfqptngvgyqp
    yrvvvlsfellhapatvcgpkkstnlvknkcvnfnfngltgtgvltesnkkflpfqqfgr
    diadttdavrdpqtleilditpcsfggvsvitpgtntsnqvavlyqdvnctevnvfqtra
    gcligaehvnnsyecdipigagicasyqtsqsiiaytmslgaensvaysnnsiaiptnft
    isvtteilpvsmtktsvdctmyicgdstecsnlllqygsfctqlnraltgiaveqdkntq
    evfaqvkqiyktppikdfggfnfsqilpdpskpskrsfiedllfnkvtkfngltvlppll
    tdemiaqytsallagtitsgwtfgagaalqipfamqmayrfngigvtqnvlyenqklian
    qfnsaigkiqdslsstasalgklqdvvnqnaqalntlvkqlssnfgaissvlndilsrld
    ppeaevqidrlitgrlqslqtyvtqqliraaeirasanlaatkmsecvlgqskrvdfcgk
    gyhlmsfpqsaphgvvflhvtyvpaqeknfttapaichdgkahfpregvfvsngthwfvt
    qrnfyepqiittdntfvsgncdvvigivnntvydplqpelds
    

  • Chain 'G':
    Sequence, based on SEQRES records:
    >7k8yG (G:)
    qvqlvqsgaevkkpgasvkvsckasgytftgyymhwvrqapgqglewmgwispvsggtny
    aqkfqgrvtmtrdtsistaymelsrlrsddtavyycaraplfptgvlagdyyyygmdvwg
    qgttvtvssastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvh
    tfpavlqssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkrvepkscdkthhhhh
    h
    

    Sequence, based on observed residues (ATOM records):
    >7k8yG (G:)
    qvqlvqsgaevkkpgasvkvsckasgytftgyymhwvrqapgqglewmgwispvsggtny
    aqkfqgrvtmtrdtsistaymelsrlrsddtavyycaraplfptgvlagdyyyygmdvwg
    qgttvtvs
    

  • Chain 'I':
    Sequence, based on SEQRES records:
    >7k8yI (I:)
    qsaltqpasvsgspgqsitisctgtssdvgsynlvswyqqhpgkapklmiyegskrpsgv
    snrfsgsksgntasltisglqaedeadyyccsyagsstlvfgggtkltvlgqpkaapsvt
    lfppsseelqankatlvclisdfypgavtvawkadsspvkagvetttpskqsnnkyaass
    ylsltpeqwkshrsyscqvthegstvektvaptecs
    

    Sequence, based on observed residues (ATOM records):
    >7k8yI (I:)
    altqpasvsgspgqsitisctgtssdvgsynlvswyqqhpgkapklmiyegskrpsgvsn
    rfsgsksgntasltisglqaedeadyyccsyagsstlvfgggtkltvl