PDB entry 7dk4

View 7dk4 on RCSB PDB site
Description: s-2h2-f3a structure, two rbds are up and one rbd is down, each rbd binds with a 2h2 fab.
Deposited on 2020-11-23, released 2020-12-02
The last revision was dated 2021-03-10, with a file datestamp of 2021-03-05.
Experiment type: EM
Resolution: 3.8 Å
R-factor: N/A
AEROSPACI score: 0.16 (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
      • conflict (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
      • conflict (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
      • conflict (985-986)
  • Chain 'a':
    Compound: The heavy chain of 2H2 Fab
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 7DK4 (0-213)
  • Chain 'b':
    Compound: The light chain of 2H2 Fab
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 7DK4 (0-217)
  • Chain 'c':
    Compound: The heavy chain of 2H2 Fab
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 7DK4 (0-213)
  • Chain 'd':
    Compound: The light chain of 2H2 Fab
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 7DK4 (0-217)
  • Chain 'e':
    Compound: The heavy chain of 2H2 Fab
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 7DK4 (0-213)
  • Chain 'f':
    Compound: The light chain of 2H2 Fab
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 7DK4 (0-217)

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:
    >7dk4A (A:)
mfvflvllplvssqcvnlttrtqlppaytnsftrgvyypdkvfrssvlhstqdlflpffs
nvtwfhaihvsgtngtkrfdnpvlpfndgvyfasteksniirgwifgttldsktqslliv
nnatnvvikvcefqfcndpflgvyyhknnkswmesefrvyssannctfeyvsqpflmdle
gkqgnfknlrefvfknidgyfkiyskhtpinlvrdlpqgfsaleplvdlpiginitrfqt
llalhrsyltpgdsssgwtagaaayyvgylqprtfllkynengtitdavdcaldplsetk
ctlksftvekgiyqtsnfrvqptesivrfpnitnlcpfgevfnatrfasvyawnrkrisn
cvadysvlynsasfstfkcygvsptklndlcftnvyadsfvirgdevrqiapgqtgkiad
ynyklpddftgcviawnsnnldskvggnynylyrlfrksnlkpferdisteiyqagstpc
ngvegfncyfplqsygfqptngvgyqpyrvvvlsfellhapatvcgpkkstnlvknkcvn
fnfngltgtgvltesnkkflpfqqfgrdiadttdavrdpqtleilditpcsfggvsvitp
gtntsnqvavlyqdvnctevpvaihadqltptwrvystgsnvfqtragcligaehvnnsy
ecdipigagicasyqtqtnspgsassvasqsiiaytmslgaensvaysnnsiaiptnfti
svtteilpvsmtktsvdctmyicgdstecsnlllqygsfctqlnraltgiaveqdkntqe
vfaqvkqiyktppikdfggfnfsqilpdpskpskrsfiedllfnkvtladagfikqygdc
lgdiaardlicaqkfngltvlpplltdemiaqytsallagtitsgwtfgagaalqipfam
qmayrfngigvtqnvlyenqklianqfnsaigkiqdslsstasalgklqdvvnqnaqaln
tlvkqlssnfgaissvlndilsrldppeaevqidrlitgrlqslqtyvtqqliraaeira
sanlaatkmsecvlgqskrvdfcgkgyhlmsfpqsaphgvvflhvtyvpaqeknfttapa
ichdgkahfpregvfvsngthwfvtqrnfyepqiittdntfvsgncdvvigivnntvydp
lqpeldsfkeeldkyfknhtspdvdlgdisginasvvniqkeidrlnevaknlneslidl
qelgkyeqgsgyipeaprdgqayvrkdgewvllstflenlyfqgdykddddkhhhhhhhh
h

    Sequence, based on observed residues (ATOM records):
    >7dk4A (A:)
qcvnlttrtqlppaytnsftrgvyypdkvfrssvlhstqdlflpffsnvtwfhaihrfdn
pvlpfndgvyfasteksniirgwifgttldsktqsllivnnatnvvikvcefqfcndpfl
gvyyhknnkswmesefrvyssannctfeyvsqpflmdlegkqgnfknlrefvfknidgyf
kiyskhtpinlvrdlpqgfsaleplvdlpiginitrfqtllalhrsssgwtagaaayyvg
ylqprtfllkynengtitdavdcaldplsetkctlksftvekgiyqtsnfrvqptesivr
fpnitnlcpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygvsptkln
dlcftnvyadsfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnldskvggn
ynylyrlfrksnlkpferdisteiyqagstpcngvegfncyfplqsygfqptngvgyqpy
rvvvlsfellhapatvcgpkkstnlvknkcvnfnfngltgtgvltesnkkflpfqqfgrd
iadttdavrdpqtleilditpcsfggvsvitpgtntsnqvavlyqdvnctevnvfqtrag
cligaehvnnsyecdipigagicasyqtqsiiaytmslgaensvaysnnsiaiptnftis
vtteilpvsmtktsvdctmyicgdstecsnlllqygsfctqlnraltgiaveqdkntqev
faqvkqiyktppikdfggfnfsqilpdpskskrsfiedllfnkvtfngltvlpplltdem
iaqytsallagtitsgwtfgagaalqipfamqmayrfngigvtqnvlyenqklianqfns
aigkiqdslsstasalgklqdvvnqnaqalntlvkqlssnfgaissvlndilsrldppea
evqidrlitgrlqslqtyvtqqliraaeirasanlaatkmsecvlgqskrvdfcgkgyhl
msfpqsaphgvvflhvtyvpaqeknfttapaichdgkahfpregvfvsngthwfvtqrnf
yepqiittdntfvsgncdvvigivnntvydplqpelds

  • Chain 'B':
    Sequence, based on SEQRES records:
    >7dk4B (B:)
mfvflvllplvssqcvnlttrtqlppaytnsftrgvyypdkvfrssvlhstqdlflpffs
nvtwfhaihvsgtngtkrfdnpvlpfndgvyfasteksniirgwifgttldsktqslliv
nnatnvvikvcefqfcndpflgvyyhknnkswmesefrvyssannctfeyvsqpflmdle
gkqgnfknlrefvfknidgyfkiyskhtpinlvrdlpqgfsaleplvdlpiginitrfqt
llalhrsyltpgdsssgwtagaaayyvgylqprtfllkynengtitdavdcaldplsetk
ctlksftvekgiyqtsnfrvqptesivrfpnitnlcpfgevfnatrfasvyawnrkrisn
cvadysvlynsasfstfkcygvsptklndlcftnvyadsfvirgdevrqiapgqtgkiad
ynyklpddftgcviawnsnnldskvggnynylyrlfrksnlkpferdisteiyqagstpc
ngvegfncyfplqsygfqptngvgyqpyrvvvlsfellhapatvcgpkkstnlvknkcvn
fnfngltgtgvltesnkkflpfqqfgrdiadttdavrdpqtleilditpcsfggvsvitp
gtntsnqvavlyqdvnctevpvaihadqltptwrvystgsnvfqtragcligaehvnnsy
ecdipigagicasyqtqtnspgsassvasqsiiaytmslgaensvaysnnsiaiptnfti
svtteilpvsmtktsvdctmyicgdstecsnlllqygsfctqlnraltgiaveqdkntqe
vfaqvkqiyktppikdfggfnfsqilpdpskpskrsfiedllfnkvtladagfikqygdc
lgdiaardlicaqkfngltvlpplltdemiaqytsallagtitsgwtfgagaalqipfam
qmayrfngigvtqnvlyenqklianqfnsaigkiqdslsstasalgklqdvvnqnaqaln
tlvkqlssnfgaissvlndilsrldppeaevqidrlitgrlqslqtyvtqqliraaeira
sanlaatkmsecvlgqskrvdfcgkgyhlmsfpqsaphgvvflhvtyvpaqeknfttapa
ichdgkahfpregvfvsngthwfvtqrnfyepqiittdntfvsgncdvvigivnntvydp
lqpeldsfkeeldkyfknhtspdvdlgdisginasvvniqkeidrlnevaknlneslidl
qelgkyeqgsgyipeaprdgqayvrkdgewvllstflenlyfqgdykddddkhhhhhhhh
h

    Sequence, based on observed residues (ATOM records):
    >7dk4B (B:)
qcvnlttrtqlppaytnsftrgvyypdkvfrssvlhstqdlflpffsnvtwfhaihrfdn
pvlpfndgvyfasteksniirgwifgttldsktqsllivnnatnvvikvcefqfcndpfl
gvyyhknnkswmesefrvyssannctfeyvsqpflmdlegkqgnfknlrefvfknidgyf
kiyskhtpinlvrdlpqgfsaleplvdlpiginitrfqtllalhrsssgwtagaaayyvg
ylqprtfllkynengtitdavdcaldplsetkctlksftvekgiyqtsnfrvqptesivr
fpnitnlcpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygvsptkln
dlcftnvyadsfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnldskvggn
ynylyrlfrksnlkpferdisteiyqagstpcngvegfncyfplqsygfqptngvgyqpy
rvvvlsfellhapatvcgpkkstnlvknkcvnfnfngltgtgvltesnkkflpfqqfgrd
iadttdavrdpqtleilditpcsfggvsvitpgtntsnqvavlyqdvnctevnvfqtrag
cligaehvnnsyecdipigagicasyqtqsiiaytmslgaensvaysnnsiaiptnftis
vtteilpvsmtktsvdctmyicgdstecsnlllqygsfctqlnraltgiaveqdkntqev
faqvkqiyktppikdfggfnfsqilpdpskskrsfiedllfnkvtfngltvlpplltdem
iaqytsallagtitsgwtfgagaalqipfamqmayrfngigvtqnvlyenqklianqfns
aigkiqdslsstasalgklqdvvnqnaqalntlvkqlssnfgaissvlndilsrldppea
evqidrlitgrlqslqtyvtqqliraaeirasanlaatkmsecvlgqskrvdfcgkgyhl
msfpqsaphgvvflhvtyvpaqeknfttapaichdgkahfpregvfvsngthwfvtqrnf
yepqiittdntfvsgncdvvigivnntvydplqpelds

  • Chain 'C':
    Sequence, based on SEQRES records:
    >7dk4C (C:)
mfvflvllplvssqcvnlttrtqlppaytnsftrgvyypdkvfrssvlhstqdlflpffs
nvtwfhaihvsgtngtkrfdnpvlpfndgvyfasteksniirgwifgttldsktqslliv
nnatnvvikvcefqfcndpflgvyyhknnkswmesefrvyssannctfeyvsqpflmdle
gkqgnfknlrefvfknidgyfkiyskhtpinlvrdlpqgfsaleplvdlpiginitrfqt
llalhrsyltpgdsssgwtagaaayyvgylqprtfllkynengtitdavdcaldplsetk
ctlksftvekgiyqtsnfrvqptesivrfpnitnlcpfgevfnatrfasvyawnrkrisn
cvadysvlynsasfstfkcygvsptklndlcftnvyadsfvirgdevrqiapgqtgkiad
ynyklpddftgcviawnsnnldskvggnynylyrlfrksnlkpferdisteiyqagstpc
ngvegfncyfplqsygfqptngvgyqpyrvvvlsfellhapatvcgpkkstnlvknkcvn
fnfngltgtgvltesnkkflpfqqfgrdiadttdavrdpqtleilditpcsfggvsvitp
gtntsnqvavlyqdvnctevpvaihadqltptwrvystgsnvfqtragcligaehvnnsy
ecdipigagicasyqtqtnspgsassvasqsiiaytmslgaensvaysnnsiaiptnfti
svtteilpvsmtktsvdctmyicgdstecsnlllqygsfctqlnraltgiaveqdkntqe
vfaqvkqiyktppikdfggfnfsqilpdpskpskrsfiedllfnkvtladagfikqygdc
lgdiaardlicaqkfngltvlpplltdemiaqytsallagtitsgwtfgagaalqipfam
qmayrfngigvtqnvlyenqklianqfnsaigkiqdslsstasalgklqdvvnqnaqaln
tlvkqlssnfgaissvlndilsrldppeaevqidrlitgrlqslqtyvtqqliraaeira
sanlaatkmsecvlgqskrvdfcgkgyhlmsfpqsaphgvvflhvtyvpaqeknfttapa
ichdgkahfpregvfvsngthwfvtqrnfyepqiittdntfvsgncdvvigivnntvydp
lqpeldsfkeeldkyfknhtspdvdlgdisginasvvniqkeidrlnevaknlneslidl
qelgkyeqgsgyipeaprdgqayvrkdgewvllstflenlyfqgdykddddkhhhhhhhh
h

    Sequence, based on observed residues (ATOM records):
    >7dk4C (C:)
qcvnlttrtqlppaytnsftrgvyypdkvfrssvlhstqdlflpffsnvtwfhaihrfdn
pvlpfndgvyfasteksniirgwifgttldsktqsllivnnatnvvikvcefqfcndpfl
gvyyhknnkswmesefrvyssannctfeyvsqpflmdlegkqgnfknlrefvfknidgyf
kiyskhtpinlvrdlpqgfsaleplvdlpiginitrfqtllalhrsssgwtagaaayyvg
ylqprtfllkynengtitdavdcaldplsetkctlksftvekgiyqtsnfrvqptesivr
fpnitnlcpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygvsptkln
dlcftnvyadsfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnldskvggn
ynylyrlfrksnlkpferdisteiyqagstpcngvegfncyfplqsygfqptngvgyqpy
rvvvlsfellhapatvcgpkkstnlvknkcvnfnfngltgtgvltesnkkflpfqqfgrd
iadttdavrdpqtleilditpcsfggvsvitpgtntsnqvavlyqdvnctevnvfqtrag
cligaehvnnsyecdipigagicasyqtqsiiaytmslgaensvaysnnsiaiptnftis
vtteilpvsmtktsvdctmyicgdstecsnlllqygsfctqlnraltgiaveqdkntqev
faqvkqiyktppikdfggfnfsqilpdpskskrsfiedllfnkvtfngltvlpplltdem
iaqytsallagtitsgwtfgagaalqipfamqmayrfngigvtqnvlyenqklianqfns
aigkiqdslsstasalgklqdvvnqnaqalntlvkqlssnfgaissvlndilsrldppea
evqidrlitgrlqslqtyvtqqliraaeirasanlaatkmsecvlgqskrvdfcgkgyhl
msfpqsaphgvvflhvtyvpaqeknfttapaichdgkahfpregvfvsngthwfvtqrnf
yepqiittdntfvsgncdvvigivnntvydplqpelds

  • Chain 'a':
    Sequence; same for both SEQRES and ATOM records:
    >7dk4a (a:)
qvqlkqsgpslvqpsqslsitctvsgfsltsygvhwvrqspgkglewlgvmwrggntdyn
aafmsrlsitkdnsksqvffkmnslqtddtaiyycaknggahamdfwgqgtsvtvssakt
tppsvyplapgsaaqtnsmvtlgclvkgyfpepvtvtwnsgslssgvhtfpavlqsdlyt
lsssvtvpsstwpsetvtcnvahpasstkvdkki

  • Chain 'b':
    Sequence; same for both SEQRES and ATOM records:
    >7dk4b (b:)
nivltqspaslavslgqratiscrasesvdsygnsflhwyqqkpgqppklliylasnles
gvparfsgsgsrtdftltidpveaddaatyycqqnnedpftfgsgtkleikradaaptvs
ifppsseqltsggasvvcflnnfypkdinvkwkidgserqngvlnswtdqdskdstysms
stltltkdeyerhnsytceathktstspivksfnrnec

  • Chain 'c':
    Sequence; same for both SEQRES and ATOM records:
    >7dk4c (c:)
qvqlkqsgpslvqpsqslsitctvsgfsltsygvhwvrqspgkglewlgvmwrggntdyn
aafmsrlsitkdnsksqvffkmnslqtddtaiyycaknggahamdfwgqgtsvtvssakt
tppsvyplapgsaaqtnsmvtlgclvkgyfpepvtvtwnsgslssgvhtfpavlqsdlyt
lsssvtvpsstwpsetvtcnvahpasstkvdkki

  • Chain 'd':
    Sequence; same for both SEQRES and ATOM records:
    >7dk4d (d:)
nivltqspaslavslgqratiscrasesvdsygnsflhwyqqkpgqppklliylasnles
gvparfsgsgsrtdftltidpveaddaatyycqqnnedpftfgsgtkleikradaaptvs
ifppsseqltsggasvvcflnnfypkdinvkwkidgserqngvlnswtdqdskdstysms
stltltkdeyerhnsytceathktstspivksfnrnec

  • Chain 'e':
    Sequence; same for both SEQRES and ATOM records:
    >7dk4e (e:)
qvqlkqsgpslvqpsqslsitctvsgfsltsygvhwvrqspgkglewlgvmwrggntdyn
aafmsrlsitkdnsksqvffkmnslqtddtaiyycaknggahamdfwgqgtsvtvssakt
tppsvyplapgsaaqtnsmvtlgclvkgyfpepvtvtwnsgslssgvhtfpavlqsdlyt
lsssvtvpsstwpsetvtcnvahpasstkvdkki

  • Chain 'f':
    Sequence; same for both SEQRES and ATOM records:
    >7dk4f (f:)
nivltqspaslavslgqratiscrasesvdsygnsflhwyqqkpgqppklliylasnles
gvparfsgsgsrtdftltidpveaddaatyycqqnnedpftfgsgtkleikradaaptvs
ifppsseqltsggasvvcflnnfypkdinvkwkidgserqngvlnswtdqdskdstysms
stltltkdeyerhnsytceathktstspivksfnrnec