PDB entry 7l2d

View 7l2d on RCSB PDB site
Description: cryo-em structure of ntd-directed neutralizing antibody 1-87 in complex with prefusion sars-cov-2 spike glycoprotein
Deposited on 2020-12-16, released 2021-03-24
The last revision was dated 2021-05-26, with a file datestamp of 2021-05-21.
Experiment type: EM
Resolution: 3.55 Å
R-factor: N/A
AEROSPACI score: 0.15 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Spike glycoprotein
    Species: Severe acute respiratory syndrome coronavirus 2 [TaxId:2697049]
    Gene: S, 2
    Database cross-references and differences (RAF-indexed):
    • Uniprot P0DTC2
      • engineered mutation (985-986)
  • 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
      • engineered mutation (985-986)
  • Chain 'C':
    Compound: Spike glycoprotein
    Species: Severe acute respiratory syndrome coronavirus 2 [TaxId:2697049]
    Gene: S, 2
    Database cross-references and differences (RAF-indexed):
    • Uniprot P0DTC2
      • engineered mutation (985-986)
  • Chain 'H':
    Compound: 1-87 heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7L2D (0-End)
  • Chain 'L':
    Compound: 1-87 light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7L2D (0-End)
  • Heterogens: BMA, 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 'A':
    Sequence, based on SEQRES records:
    >7l2dA (A:)
mfvflvllplvssqcvnlttrtqlppaytnsftrgvyypdkvfrssvlhstqdlflpffs
nvtwfhaihvsgtngtkrfdnpvlpfndgvyfasteksniirgwifgttldsktqslliv
nnatnvvikvcefqfcndpflgvyyhknnkswmesefrvyssannctfeyvsqpflmdle
gkqgnfknlrefvfknidgyfkiyskhtpinlvrdlpqgfsaleplvdlpiginitrfqt
llalhrsyltpgdsssgwtagaaayyvgylqprtfllkynengtitdavdcaldplsetk
ctlksftvekgiyqtsnfrvqptesivrfpnitnlcpfgevfnatrfasvyawnrkrisn
cvadysvlynsasfstfkcygvsptklndlcftnvyadsfvirgdevrqiapgqtgkiad
ynyklpddftgcviawnsnnldskvggnynylyrlfrksnlkpferdisteiyqagstpc
ngvegfncyfplqsygfqptngvgyqpyrvvvlsfellhapatvcgpkkstnlvknkcvn
fnfngltgtgvltesnkkflpfqqfgrdiadttdavrdpqtleilditpcsfggvsvitp
gtntsnqvavlyqdvnctevpvaihadqltptwrvystgsnvfqtragcligaehvnnsy
ecdipigagicasyqtqtnspgsassvasqsiiaytmslgaensvaysnnsiaiptnfti
svtteilpvsmtktsvdctmyicgdstecsnlllqygsfctqlnraltgiaveqdkntqe
vfaqvkqiyktppikdfggfnfsqilpdpskpskrsfiedllfnkvtladagfikqygdc
lgdiaardlicaqkfngltvlpplltdemiaqytsallagtitsgwtfgagaalqipfam
qmayrfngigvtqnvlyenqklianqfnsaigkiqdslsstasalgklqdvvnqnaqaln
tlvkqlssnfgaissvlndilsrldppeaevqidrlitgrlqslqtyvtqqliraaeira
sanlaatkmsecvlgqskrvdfcgkgyhlmsfpqsaphgvvflhvtyvpaqeknfttapa
ichdgkahfpregvfvsngthwfvtqrnfyepqiittdntfvsgncdvvigivnntvydp
lqpeldsfkeeldkyfknhtspdvdlgdisginasvvniqkeidrlnevaknlneslidl
qelgkyeqgsgyipeaprdgqayvrkdgewvllstflgrslevlfqgpghhhhhhhhsaw
shpqfekgggsggggsggsawshpqfek

    Sequence, based on observed residues (ATOM records):
    >7l2dA (A:)
qcvnlttrtqlppaytnsftrgvyypdkvfrssvlhstqdlflpffsnvtwfhaihvsgt
ngtkrfdnpvlpfndgvyfasteksniirgwifgttldsktqsllivnnatnvvikvcef
qfcndpflgvyyhknnkswmesefrvyssannctfeyvsqpflmdlegkqgnfknlrefv
fknidgyfkiyskhtpinlvrdlpqgfsaleplvdlpiginitrfqtllalhrsyltpgd
sssgwtagaaayyvgylqprtfllkynengtitdavdcaldplsetkctlksftvekgiy
qtsnfrvqptesivrfpnitnlcpfgevfnatrfasvyawnrkrisncvadysvlynsas
fstfkcygvsptklndlcftnvyadsfvirgdevrqiapgqtgkiadynyklpddftgcv
iawnsnnldskvggnynylyrlfrksnlkpferdisteiyqagstpcngvegfncyfplq
sygfqptngvgyqpyrvvvlsfellhapatvcgpkkstnlvknkcvnfnfngltgtgvlt
esnkkflpfqqfgrdiadttdavrdpqtleilditpcsfggvsvitpgtntsnqvavlyq
dvnctevpvaihadqltptwrvystgsnvfqtragcligaehvnnsyecdipigagicas
yqtsqsiiaytmslgaensvaysnnsiaiptnftisvtteilpvsmtktsvdctmyicgd
stecsnlllqygsfctqlnraltgiaveqdkntqevfaqvkqiyktppikdfggfnfsqi
lpdpskpskrsfiedllfnkvtlaaqkfngltvlpplltdemiaqytsallagtitsgwt
fgagaalqipfamqmayrfngigvtqnvlyenqklianqfnsaigkiqdslsstasalgk
lqdvvnqnaqalntlvkqlssnfgaissvlndilsrldppeaevqidrlitgrlqslqty
vtqqliraaeirasanlaatkmsecvlgqskrvdfcgkgyhlmsfpqsaphgvvflhvty
vpaqeknfttapaichdgkahfpregvfvsngthwfvtqrnfyepqiittdntfvsgncd
vvigivnntvydplqpelds

  • Chain 'B':
    Sequence, based on SEQRES records:
    >7l2dB (B:)
mfvflvllplvssqcvnlttrtqlppaytnsftrgvyypdkvfrssvlhstqdlflpffs
nvtwfhaihvsgtngtkrfdnpvlpfndgvyfasteksniirgwifgttldsktqslliv
nnatnvvikvcefqfcndpflgvyyhknnkswmesefrvyssannctfeyvsqpflmdle
gkqgnfknlrefvfknidgyfkiyskhtpinlvrdlpqgfsaleplvdlpiginitrfqt
llalhrsyltpgdsssgwtagaaayyvgylqprtfllkynengtitdavdcaldplsetk
ctlksftvekgiyqtsnfrvqptesivrfpnitnlcpfgevfnatrfasvyawnrkrisn
cvadysvlynsasfstfkcygvsptklndlcftnvyadsfvirgdevrqiapgqtgkiad
ynyklpddftgcviawnsnnldskvggnynylyrlfrksnlkpferdisteiyqagstpc
ngvegfncyfplqsygfqptngvgyqpyrvvvlsfellhapatvcgpkkstnlvknkcvn
fnfngltgtgvltesnkkflpfqqfgrdiadttdavrdpqtleilditpcsfggvsvitp
gtntsnqvavlyqdvnctevpvaihadqltptwrvystgsnvfqtragcligaehvnnsy
ecdipigagicasyqtqtnspgsassvasqsiiaytmslgaensvaysnnsiaiptnfti
svtteilpvsmtktsvdctmyicgdstecsnlllqygsfctqlnraltgiaveqdkntqe
vfaqvkqiyktppikdfggfnfsqilpdpskpskrsfiedllfnkvtladagfikqygdc
lgdiaardlicaqkfngltvlpplltdemiaqytsallagtitsgwtfgagaalqipfam
qmayrfngigvtqnvlyenqklianqfnsaigkiqdslsstasalgklqdvvnqnaqaln
tlvkqlssnfgaissvlndilsrldppeaevqidrlitgrlqslqtyvtqqliraaeira
sanlaatkmsecvlgqskrvdfcgkgyhlmsfpqsaphgvvflhvtyvpaqeknfttapa
ichdgkahfpregvfvsngthwfvtqrnfyepqiittdntfvsgncdvvigivnntvydp
lqpeldsfkeeldkyfknhtspdvdlgdisginasvvniqkeidrlnevaknlneslidl
qelgkyeqgsgyipeaprdgqayvrkdgewvllstflgrslevlfqgpghhhhhhhhsaw
shpqfekgggsggggsggsawshpqfek

    Sequence, based on observed residues (ATOM records):
    >7l2dB (B:)
qcvnlttrtqlppaytnsftrgvyypdkvfrssvlhstqdlflpffsnvtwfhaihkrfd
npvlpfndgvyfasteksniirgwifgttldsktqsllivnnatnvvikvcefqfcndpf
lgvyyhknnkswmesefrvyssannctfeyvsqpflmdlgnfknlrefvfknidgyfkiy
skhtpinlvrdlpqgfsaleplvdlpiginitrfqtllalhrgwtagaaayyvgylqprt
fllkynengtitdavdcaldplsetkctlksftvekgiyqtsnfrvqptesivrfpnitn
lcpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygvsptklndlcftn
vyadsfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnldskvggnynylyr
lfrksnlkpferdisteiyqagstpcngvegfncyfplqsygfqptngvgyqpyrvvvls
fellhapatvcgpkkstnlvknkcvnfnfngltgtgvltesnkkflpfqqfgrdiadttd
avrdpqtleilditpcsfggvsvitpgtntsnqvavlyqdvnctevpvaihadqltptwr
vystgsnvfqtragcligaehvnnsyecdipigagicasyqtsqsiiaytmslgaensva
ysnnsiaiptnftisvtteilpvsmtktsvdctmyicgdstecsnlllqygsfctqlnra
ltgiaveqdkntqevfaqvkqiyktppikdfggfnfsqilpdpskpskrsfiedllfnkv
tlaqkfngltvlpplltdemiaqytsallagtitsgwtfgagaalqipfamqmayrfngi
gvtqnvlyenqklianqfnsaigkiqdslsstasalgklqdvvnqnaqalntlvkqlssn
fgaissvlndilsrldppeaevqidrlitgrlqslqtyvtqqliraaeirasanlaatkm
secvlgqskrvdfcgkgyhlmsfpqsaphgvvflhvtyvpaqeknfttapaichdgkahf
pregvfvsngthwfvtqrnfyepqiittdntfvsgncdvvigivnntvydplqpelds

  • Chain 'C':
    Sequence, based on SEQRES records:
    >7l2dC (C:)
mfvflvllplvssqcvnlttrtqlppaytnsftrgvyypdkvfrssvlhstqdlflpffs
nvtwfhaihvsgtngtkrfdnpvlpfndgvyfasteksniirgwifgttldsktqslliv
nnatnvvikvcefqfcndpflgvyyhknnkswmesefrvyssannctfeyvsqpflmdle
gkqgnfknlrefvfknidgyfkiyskhtpinlvrdlpqgfsaleplvdlpiginitrfqt
llalhrsyltpgdsssgwtagaaayyvgylqprtfllkynengtitdavdcaldplsetk
ctlksftvekgiyqtsnfrvqptesivrfpnitnlcpfgevfnatrfasvyawnrkrisn
cvadysvlynsasfstfkcygvsptklndlcftnvyadsfvirgdevrqiapgqtgkiad
ynyklpddftgcviawnsnnldskvggnynylyrlfrksnlkpferdisteiyqagstpc
ngvegfncyfplqsygfqptngvgyqpyrvvvlsfellhapatvcgpkkstnlvknkcvn
fnfngltgtgvltesnkkflpfqqfgrdiadttdavrdpqtleilditpcsfggvsvitp
gtntsnqvavlyqdvnctevpvaihadqltptwrvystgsnvfqtragcligaehvnnsy
ecdipigagicasyqtqtnspgsassvasqsiiaytmslgaensvaysnnsiaiptnfti
svtteilpvsmtktsvdctmyicgdstecsnlllqygsfctqlnraltgiaveqdkntqe
vfaqvkqiyktppikdfggfnfsqilpdpskpskrsfiedllfnkvtladagfikqygdc
lgdiaardlicaqkfngltvlpplltdemiaqytsallagtitsgwtfgagaalqipfam
qmayrfngigvtqnvlyenqklianqfnsaigkiqdslsstasalgklqdvvnqnaqaln
tlvkqlssnfgaissvlndilsrldppeaevqidrlitgrlqslqtyvtqqliraaeira
sanlaatkmsecvlgqskrvdfcgkgyhlmsfpqsaphgvvflhvtyvpaqeknfttapa
ichdgkahfpregvfvsngthwfvtqrnfyepqiittdntfvsgncdvvigivnntvydp
lqpeldsfkeeldkyfknhtspdvdlgdisginasvvniqkeidrlnevaknlneslidl
qelgkyeqgsgyipeaprdgqayvrkdgewvllstflgrslevlfqgpghhhhhhhhsaw
shpqfekgggsggggsggsawshpqfek

    Sequence, based on observed residues (ATOM records):
    >7l2dC (C:)
qcvnlttrtqlppaytnsftrgvyypdkvfrssvlhstqdlflpffsnvtwfhaihkrfd
npvlpfndgvyfasteksniirgwifgttldsktqsllivnnatnvvikvcefqfcndpf
lgvyyhknnkswmesefrvyssannctfeyvsqpflmdlgnfknlrefvfknidgyfkiy
skhtpinlvrdlpqgfsaleplvdlpiginitrfqtllalhrgwtagaaayyvgylqprt
fllkynengtitdavdcaldplsetkctlksftvekgiyqtsnfrvqptesivrfpnitn
lcpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygvsptklndlcftn
vyadsfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnldskvggnynylyr
lfrksnlkpferdisteiyqagstpcngvegfncyfplqsygfqptngvgyqpyrvvvls
fellhapatvcgpkkstnlvknkcvnfnfngltgtgvltesnkkflpfqqfgrdiadttd
avrdpqtleilditpcsfggvsvitpgtntsnqvavlyqdvnctevpvaihadqltptwr
vystgsnvfqtragcligaehvnnsyecdipigagicasyqtsqsiiaytmslgaensva
ysnnsiaiptnftisvtteilpvsmtktsvdctmyicgdstecsnlllqygsfctqlnra
ltgiaveqdkntqevfaqvkqiyktppikdfggfnfsqilpdpskpskrsfiedllfnkv
tlaqkfngltvlpplltdemiaqytsallagtitsgwtfgagaalqipfamqmayrfngi
gvtqnvlyenqklianqfnsaigkiqdslsstasalgklqdvvnqnaqalntlvkqlssn
fgaissvlndilsrldppeaevqidrlitgrlqslqtyvtqqliraaeirasanlaatkm
secvlgqskrvdfcgkgyhlmsfpqsaphgvvflhvtyvpaqeknfttapaichdgkahf
pregvfvsngthwfvtqrnfyepqiittdntfvsgncdvvigivnntvydplqpelds

  • Chain 'H':
    Sequence, based on SEQRES records:
    >7l2dH (H:)
qvqlvqsgaevkkpgasvkvsckvsgytlielsmhwvrqapgkglewmggfdpedaetiy
aqkfqgrvtmtedtstdtaymelsslrsedtavyycatgiavigpppstyyyygmdvwgq
gttvtvssastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvht
fpavlqssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepkscdkth

    Sequence, based on observed residues (ATOM records):
    >7l2dH (H:)
qvqlvqsgaevkkpgasvkvsckvsgytlielsmhwvrqapgkglewmggfdpedaetiy
aqkfqgrvtmtedtstdtaymelsslrsedtavyycatgiavigpppstyyyygmdvwgq
gttvtvs

  • Chain 'L':
    Sequence, based on SEQRES records:
    >7l2dL (L:)
qsaltqpasvsgspgqsitisctgtssdvggynyvswyqqhpgkapklmiydvskrpsgv
snrfsgsksgntasltisglqaedeadyycssytssstyvfgtgtkvtvlgqpkaapsvt
lfppsseelqankatlvclisdfypgavtvawkadsspvkagvetttpskqsnnkyaass
ylsltpeqwkshrsyscqvthegstvektvaptec

    Sequence, based on observed residues (ATOM records):
    >7l2dL (L:)
qsaltqpasvsgspgqsitisctgtssdvggynyvswyqqhpgkapklmiydvskrpsgv
snrfsgsksgntasltisglqaedeadyycssytssstyvfgtgtkvtv