PDB entry 7nd3

View 7nd3 on RCSB PDB site
Description: em structure of sars-cov-2 spike glycoprotein in complex with covox-40 fab
Deposited on 2021-01-30, released 2021-03-03
The last revision was dated 2021-04-28, with a file datestamp of 2021-04-23.
Experiment type: EM
Resolution: 3.7 Å
R-factor: N/A
AEROSPACI score: 0.14 (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: COVOX-40 heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7ND3
  • Chain 'L':
    Compound: COVOX-40 light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7ND3
  • 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 'A':
    Sequence, based on SEQRES records:
    >7nd3A (A:)
mfvflvllplvssqcvnlttrtqlppaytnsftrgvyypdkvfrssvlhstqdlflpffs
nvtwfhaihvsgtngtkrfdnpvlpfndgvyfasteksniirgwifgttldsktqslliv
nnatnvvikvcefqfcndpflgvyyhknnkswmesefrvyssannctfeyvsqpflmdle
gkqgnfknlrefvfknidgyfkiyskhtpinlvrdlpqgfsaleplvdlpiginitrfqt
llalhrsyltpgdsssgwtagaaayyvgylqprtfllkynengtitdavdcaldplsetk
ctlksftvekgiyqtsnfrvqptesivrfpnitnlcpfgevfnatrfasvyawnrkrisn
cvadysvlynsasfstfkcygvsptklndlcftnvyadsfvirgdevrqiapgqtgkiad
ynyklpddftgcviawnsnnldskvggnynylyrlfrksnlkpferdisteiyqagstpc
ngvegfncyfplqsygfqptngvgyqpyrvvvlsfellhapatvcgpkkstnlvknkcvn
fnfngltgtgvltesnkkflpfqqfgrdiadttdavrdpqtleilditpcsfggvsvitp
gtntsnqvavlyqdvnctevpvaihadqltptwrvystgsnvfqtragcligaehvnnsy
ecdipigagicasyqtqtnspgsassvasqsiiaytmslgaensvaysnnsiaiptnfti
svtteilpvsmtktsvdctmyicgdstecsnlllqygsfctqlnraltgiaveqdkntqe
vfaqvkqiyktppikdfggfnfsqilpdpskpskrsfiedllfnkvtladagfikqygdc
lgdiaardlicaqkfngltvlpplltdemiaqytsallagtitsgwtfgagaalqipfam
qmayrfngigvtqnvlyenqklianqfnsaigkiqdslsstasalgklqdvvnqnaqaln
tlvkqlssnfgaissvlndilsrldppeaevqidrlitgrlqslqtyvtqqliraaeira
sanlaatkmsecvlgqskrvdfcgkgyhlmsfpqsaphgvvflhvtyvpaqeknfttapa
ichdgkahfpregvfvsngthwfvtqrnfyepqiittdntfvsgncdvvigivnntvydp
lqpeldsfkeeldkyfknhtspdvdlgdisginasvvniqkeidrlnevaknlneslidl
qelgkyeqgsgyipeaprdgqayvrkdgewvllstflgrslevlfqgpghhhhhhhhgsa
wshpqfekgggsgggsggsawshpqfek

    Sequence, based on observed residues (ATOM records):
    >7nd3A (A:)
aytnsftrgvyypdkvfrssvlhstqdlflpffsnvtwfhaihpvlpfndgvyfasteks
niirgwifgttldsksllivnnatnvvikvcefqfcndpflgvctfeyvsnlrefvfkni
dgyfkiyskhtpinlvrdlpqgfsaleplvdlpiginitrfqtllaayyvgylqprtfll
kynengtitdavdcaldplsetkctlksftvekgiyqtsnfrvqptesivrfpnitnlcp
fgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygvsptklndlcftnvya
dsfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnldskvggnynylyrlfr
ksnlkpferdisteiyqagstpcngvegfncyfplqsygfqptngvgyqpyrvvvlsfel
lhapatvcgpkkstnlvknkcvnfnfngltgtgvltesnkkflpfqqfgrdiadttdavr
dpqtleilditpcsfggvsvitpgtntsnqvavlyqdvnctevnvfqtragcligaehvn
nsyecdipigagicasyqtqsiiaytmslgaensvaysnnsiaiptnftisvtteilpvs
mtktsvdctmyicgdstecsnlllqygsfctqlnraltgiaveqdkntqevfaqvkqiyk
tppikdfggfnfsqilpdpskpskrsfiedllfnkvticaqkfngltvlpplltdemiaq
ytsallagtitsgwtfgagaalqipfamqmayrfngigvtqnvlyenqklianqfnsaig
kiqdslsstasalgklqdvvnqnaqalntlvkqlssnfgaissvlndilsrldppeaevq
idrlitgrlqslqtyvtqqliraaeirasanlaatkmsecvlgqskrvdfcgkgyhlmsf
pqsaphgvvflhvtyvpaqeknfttapaichdgkahfpregvfvsngthwfvtqrnfyep
qiittdntfvsgncdvvigivnntvydplqpelds

  • Chain 'B':
    Sequence, based on SEQRES records:
    >7nd3B (B:)
mfvflvllplvssqcvnlttrtqlppaytnsftrgvyypdkvfrssvlhstqdlflpffs
nvtwfhaihvsgtngtkrfdnpvlpfndgvyfasteksniirgwifgttldsktqslliv
nnatnvvikvcefqfcndpflgvyyhknnkswmesefrvyssannctfeyvsqpflmdle
gkqgnfknlrefvfknidgyfkiyskhtpinlvrdlpqgfsaleplvdlpiginitrfqt
llalhrsyltpgdsssgwtagaaayyvgylqprtfllkynengtitdavdcaldplsetk
ctlksftvekgiyqtsnfrvqptesivrfpnitnlcpfgevfnatrfasvyawnrkrisn
cvadysvlynsasfstfkcygvsptklndlcftnvyadsfvirgdevrqiapgqtgkiad
ynyklpddftgcviawnsnnldskvggnynylyrlfrksnlkpferdisteiyqagstpc
ngvegfncyfplqsygfqptngvgyqpyrvvvlsfellhapatvcgpkkstnlvknkcvn
fnfngltgtgvltesnkkflpfqqfgrdiadttdavrdpqtleilditpcsfggvsvitp
gtntsnqvavlyqdvnctevpvaihadqltptwrvystgsnvfqtragcligaehvnnsy
ecdipigagicasyqtqtnspgsassvasqsiiaytmslgaensvaysnnsiaiptnfti
svtteilpvsmtktsvdctmyicgdstecsnlllqygsfctqlnraltgiaveqdkntqe
vfaqvkqiyktppikdfggfnfsqilpdpskpskrsfiedllfnkvtladagfikqygdc
lgdiaardlicaqkfngltvlpplltdemiaqytsallagtitsgwtfgagaalqipfam
qmayrfngigvtqnvlyenqklianqfnsaigkiqdslsstasalgklqdvvnqnaqaln
tlvkqlssnfgaissvlndilsrldppeaevqidrlitgrlqslqtyvtqqliraaeira
sanlaatkmsecvlgqskrvdfcgkgyhlmsfpqsaphgvvflhvtyvpaqeknfttapa
ichdgkahfpregvfvsngthwfvtqrnfyepqiittdntfvsgncdvvigivnntvydp
lqpeldsfkeeldkyfknhtspdvdlgdisginasvvniqkeidrlnevaknlneslidl
qelgkyeqgsgyipeaprdgqayvrkdgewvllstflgrslevlfqgpghhhhhhhhgsa
wshpqfekgggsgggsggsawshpqfek

    Sequence, based on observed residues (ATOM records):
    >7nd3B (B:)
aytnsftrgvyypdkvfrssvlhstqdlflpffsnvtwfhnpvlpfndgvyfasteksni
irgwifgttldsktqsllivnnatnvvikvcefqfcndpfnnctfeyvsnlrefvfknyf
kiyskhtpidlpqgfsaleplvdlpiginitrfqtllaayyvgylqprtfllkynengti
tdavdcaldplsetkctlksftvekgiyqtsnfrvqptesivrfpnitnlcpfgevfnat
rfasvyawnrkrisncvadysvlynsasfstfkcygvsptklndlcftnvyadsfvirgd
evrqiapgqtgkiadynyklpddftgcviawnsnnldskvggnynylyrlfrksnlkpfe
rdisteiyqagstpcngvegfncyfplqsygfqptngvgyqpyrvvvlsfellhapatvc
gpkkstnlvknkcvnfnfngltgtgvltesnkkflpfqqfgrdiadttdavrdpqtleil
ditpcsfggvsvitpgtntsnqvavlyqdvnctevnvfqtragcligaehvnnsyecdip
igagicasyqtsqsiiaytmslgaensvaysnnsiaiptnftisvtteilpvsmtktsvd
ctmyicgdstecsnlllqygsfctqlnraltgiaveqdkntqevfaqvkqiyktppikdf
ggfnfsqilpdpskpskrsfiedllfnkvtlicaqkfngltvlpplltdemiaqytsall
agtitsgwtfgagaalqipfamqmayrfngigvtqnvlyenqklianqfnsaigkiqdsl
sstasalgklqdvvnqnaqalntlvkqlssnfgaissvlndilsrldppeaevqidrlit
grlqslqtyvtqqliraaeirasanlaatkmsecvlgqskrvdfcgkgyhlmsfpqsaph
gvvflhvtyvpaqeknfttapaichdgkahfpregvfvsngthwfvtqrnfyepqiittd
ntfvsgncdvvigivnntvydplqpelds

  • Chain 'C':
    Sequence, based on SEQRES records:
    >7nd3C (C:)
mfvflvllplvssqcvnlttrtqlppaytnsftrgvyypdkvfrssvlhstqdlflpffs
nvtwfhaihvsgtngtkrfdnpvlpfndgvyfasteksniirgwifgttldsktqslliv
nnatnvvikvcefqfcndpflgvyyhknnkswmesefrvyssannctfeyvsqpflmdle
gkqgnfknlrefvfknidgyfkiyskhtpinlvrdlpqgfsaleplvdlpiginitrfqt
llalhrsyltpgdsssgwtagaaayyvgylqprtfllkynengtitdavdcaldplsetk
ctlksftvekgiyqtsnfrvqptesivrfpnitnlcpfgevfnatrfasvyawnrkrisn
cvadysvlynsasfstfkcygvsptklndlcftnvyadsfvirgdevrqiapgqtgkiad
ynyklpddftgcviawnsnnldskvggnynylyrlfrksnlkpferdisteiyqagstpc
ngvegfncyfplqsygfqptngvgyqpyrvvvlsfellhapatvcgpkkstnlvknkcvn
fnfngltgtgvltesnkkflpfqqfgrdiadttdavrdpqtleilditpcsfggvsvitp
gtntsnqvavlyqdvnctevpvaihadqltptwrvystgsnvfqtragcligaehvnnsy
ecdipigagicasyqtqtnspgsassvasqsiiaytmslgaensvaysnnsiaiptnfti
svtteilpvsmtktsvdctmyicgdstecsnlllqygsfctqlnraltgiaveqdkntqe
vfaqvkqiyktppikdfggfnfsqilpdpskpskrsfiedllfnkvtladagfikqygdc
lgdiaardlicaqkfngltvlpplltdemiaqytsallagtitsgwtfgagaalqipfam
qmayrfngigvtqnvlyenqklianqfnsaigkiqdslsstasalgklqdvvnqnaqaln
tlvkqlssnfgaissvlndilsrldppeaevqidrlitgrlqslqtyvtqqliraaeira
sanlaatkmsecvlgqskrvdfcgkgyhlmsfpqsaphgvvflhvtyvpaqeknfttapa
ichdgkahfpregvfvsngthwfvtqrnfyepqiittdntfvsgncdvvigivnntvydp
lqpeldsfkeeldkyfknhtspdvdlgdisginasvvniqkeidrlnevaknlneslidl
qelgkyeqgsgyipeaprdgqayvrkdgewvllstflgrslevlfqgpghhhhhhhhgsa
wshpqfekgggsgggsggsawshpqfek

    Sequence, based on observed residues (ATOM records):
    >7nd3C (C:)
aytnsftrgvyypdkvfrssvlhstqdlflpffsnvtwfhnpvlpfndgvyfasteksni
irgwifgttldsktqsllivnnatnvvikvcefqfcndpflgvnctfeyvsnlrefvfkn
idgyfkiyskhtpinlvrdlpqgfsaleplvdlpiginitrfqtllayyvgylqprtfll
kynengtitdavdcaldplsetkctlksftvekgiyqtsnfrvqptesivrfpnitnlcp
fgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygvsptklndlcftnvya
dsfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnldskvggnynylyrlfr
ksnlkpferdisteiyqagstpcngvegfncyfplqsygfqptngvgyqpyrvvvlsfel
lhapatvcgpkkstnlvknkcvnfnfngltgtgvltesnkkflpfqqfgrdiadttdavr
dpqtleilditpcsfggvsvitpgtntsnqvavlyqdvnctevnvfqtragcligaehvn
nsyecdipigagicasyqtqsiiaytmslgaensvaysnnsiaiptnftisvtteilpvs
mtktsvdctmyicgdstecsnlllqygsfctqlnraltgiaveqdkntqevfaqvkqiyk
tppikdfggfnfsqilpdpskpskrsfiedllfnkvtkfngltvlpplltdemiaqytsa
llagtitsgwtfgagaalqipfamqmayrfngigvtqnvlyenqklianqfnsaigkiqd
slsstasalgklqdvvnqnaqalntlvkqlssnfgaissvlndilsrldppeaevqidrl
itgrlqslqtyvtqqliraaeirasanlaatkmsecvlgqskrvdfcgkgyhlmsfpqsa
phgvvflhvtyvpaqeknfttapaichdgkahfpregvfvsngthwfvtqrnfyepqiit
tdntfvsgncdvvigivnntvydplqpelds

  • Chain 'H':
    Sequence, based on SEQRES records:
    >7nd3H (H:)
ilflvatatgvhsqvqlvesggglvqpggslrlscavsgftvsrnymswvrqapgkglew
vsliysggstfyadsvkgrftisrdnskntlylqmnslraedtavyycardlfhrsgyhd
ywgqgtlvtvssastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgalts
gvhtfpavlqssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepkscdk

    Sequence, based on observed residues (ATOM records):
    >7nd3H (H:)
vqlvesggglvqpggslrlscavsgftvsrnymswvrqapgkglewvsliysggstfyad
svkgrftisrdnskntlylqmnslraedtavyycardlgyhdywgqgtlvtvs

  • Chain 'L':
    Sequence, based on SEQRES records:
    >7nd3L (L:)
ilflvatatgvhsviwmtqspsslsasvgdrvtitcqasqdinnylnwyqqkpgkapkll
ifdasnletgvpsrfsgsgsgtdftftisslqpediatyycqqydnlpafgggtkvdikr
tvaapsvfifppsdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqds
kdstyslsstltlskadyekhkvyacevthqglsspvtksfnrgec

    Sequence, based on observed residues (ATOM records):
    >7nd3L (L:)
iwmtqspsslsasvgdrvtitcqasqdinnylnwyqqkpgkapkllifdasnletgvpsr
fsgsgsgtdftftisslqpediatyycqqydnlpafgggtkvdikr