PDB entry 7k8t

View 7k8t on RCSB PDB site
Description: structure of the sars-cov-2 s 6p trimer in complex with the human neutralizing antibody fab fragment, c002 (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: 3.4 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 'H':
    Compound: C002 Fab Heavy Chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7K8T
  • Chain 'L':
    Compound: C002 Fab Light Chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7K8T (0-End)
  • Chain 'M':
    Compound: C002 Fab Heavy Chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7K8T
  • Chain 'N':
    Compound: C002 Fab Light Chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7K8T (0-End)
  • Chain 'O':
    Compound: C002 Fab Heavy Chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7K8T
  • Chain 'P':
    Compound: C002 Fab Light Chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7K8T (0-End)
  • 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:
    >7k8tA (A:)
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):
    >7k8tA (A:)
aytnsftrgvyypdkvfrssvlhstqdlflpffsnvtwfhaihrfdnpvlpfndgvyfas
teksniirgwifgttldsktqsllivnnatnvvikvcefqfcndpflgvnctfeyvsfkn
lrefvfknidgyfkiyskhtpinlvrdlpqgfsaleplvdlpiginitrfqtllalhaay
yvgylqprtfllkynengtitdavdcaldplsetkctlksftvekgiyqtsnfrvqptes
ivrfpnitnlcpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygvspt
klndlcftnvyadsfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnldskg
nynylyrlfrksnlkpferdisteiyqagstpcngvegfncyfplqsygfqptnvgyqpy
rvvvlsfellhapatvcgpkkstnlvknkcvnfnfngltgtgvltesnkkflpfqqfgrd
iadttdavrdpqtleilditpcsfggvsvitpgtntsnqvavlyqdvnctevnvfqtrag
cligaehvnnsyecdipigagicasyqtsqsiiaytmslgaensvaysnnsiaiptnfti
svtteilpvsmtktsvdctmyicgdstecsnlllqygsfctqlnraltgiaveqdkntqe
vfaqvkqiyktppikdfggfnfsqilpdpskpskrsfiedllfnkvtkfngltvlppllt
demiaqytsallagtitsgwtfgagaalqipfamqmayrfngigvtqnvlyenqklianq
fnsaigkiqdslsstasalgklqdvvnqnaqalntlvkqlssnfgaissvlndilsrldp
peaevqidrlitgrlqslqtyvtqqliraaeirasanlaatkmsecvlgqskrvdfcgkg
yhlmsfpqsaphgvvflhvtyvpaqeknfttapaichdgkahfpregvfvsngthwfvtq
rnfyepqiittdntfvsgncdvvigivnntvydplqpelds

  • Chain 'B':
    Sequence, based on SEQRES records:
    >7k8tB (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):
    >7k8tB (B:)
aytnsftrgvyypdkvfrssvlhstqdlflpffsnvtwfhaihrfdnpvlpfndgvyfas
teksniirgwifgttldsktqsllivnnatnvvikvcefqfcndpflgvnctfeyvsfkn
lrefvfknidgyfkiyskhtpinlvrdlpqgfsaleplvdlpiginitrfqtllalhaay
yvgylqprtfllkynengtitdavdcaldplsetkctlksftvekgiyqtsnfrvqptes
ivrfpnitnlcpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygvspt
klndlcftnvyadsfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnldskg
nynylyrlfrksnlkpferdisteiyqagstpcngvegfncyfplqsygfqptnvgyqpy
rvvvlsfellhapatvcgpkkstnlvknkcvnfnfngltgtgvltesnkkflpfqqfgrd
iadttdavrdpqtleilditpcsfggvsvitpgtntsnqvavlyqdvnctevnvfqtrag
cligaehvnnsyecdipigagicasyqtsqsiiaytmslgaensvaysnnsiaiptnfti
svtteilpvsmtktsvdctmyicgdstecsnlllqygsfctqlnraltgiaveqdkntqe
vfaqvkqiyktppikdfggfnfsqilpdpskpskrsfiedllfnkvtkfngltvlppllt
demiaqytsallagtitsgwtfgagaalqipfamqmayrfngigvtqnvlyenqklianq
fnsaigkiqdslsstasalgklqdvvnqnaqalntlvkqlssnfgaissvlndilsrldp
peaevqidrlitgrlqslqtyvtqqliraaeirasanlaatkmsecvlgqskrvdfcgkg
yhlmsfpqsaphgvvflhvtyvpaqeknfttapaichdgkahfpregvfvsngthwfvtq
rnfyepqiittdntfvsgncdvvigivnntvydplqpelds

  • Chain 'C':
    Sequence, based on SEQRES records:
    >7k8tC (C:)
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):
    >7k8tC (C:)
aytnsftrgvyypdkvfrssvlhstqdlflpffsnvtwfhaihrfdnpvlpfndgvyfas
teksniirgwifgttldsktqsllivnnatnvvikvcefqfcndpflgvnctfeyvsfkn
lrefvfknidgyfkiyskhtpinlvrdlpqgfsaleplvdlpiginitrfqtllalhaay
yvgylqprtfllkynengtitdavdcaldplsetkctlksftvekgiyqtsnfrvqptes
ivrfpnitnlcpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygvspt
klndlcftnvyadsfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnldskg
nynylyrlfrksnlkpferdisteiyqagstpcngvegfncyfplqsygfqptnvgyqpy
rvvvlsfellhapatvcgpkkstnlvknkcvnfnfngltgtgvltesnkkflpfqqfgrd
iadttdavrdpqtleilditpcsfggvsvitpgtntsnqvavlyqdvnctevnvfqtrag
cligaehvnnsyecdipigagicasyqtsqsiiaytmslgaensvaysnnsiaiptnfti
svtteilpvsmtktsvdctmyicgdstecsnlllqygsfctqlnraltgiaveqdkntqe
vfaqvkqiyktppikdfggfnfsqilpdpskpskrsfiedllfnkvtkfngltvlppllt
demiaqytsallagtitsgwtfgagaalqipfamqmayrfngigvtqnvlyenqklianq
fnsaigkiqdslsstasalgklqdvvnqnaqalntlvkqlssnfgaissvlndilsrldp
peaevqidrlitgrlqslqtyvtqqliraaeirasanlaatkmsecvlgqskrvdfcgkg
yhlmsfpqsaphgvvflhvtyvpaqeknfttapaichdgkahfpregvfvsngthwfvtq
rnfyepqiittdntfvsgncdvvigivnntvydplqpelds

  • Chain 'H':
    Sequence, based on SEQRES records:
    >7k8tH (H:)
evqlvesgggvvqpgrslrlscaasgftfsiygmhwvrqapgkglewvavisydgsnkyy
adsvkgrftisrdnskntlylqmnslraedtavyycakegrpsdivvvvafdywgqgtlv
tvssastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpav
lqssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkrvepkscdkthhhhhh

    Sequence, based on observed residues (ATOM records):
    >7k8tH (H:)
vqlvesgggvvqpgrslrlscaasgftfsiygmhwvrqapgkglewvavisydgsnkyya
dsvkgrftisrdnskntlylqmnslraedtavyycakegrpsdivvvvafdywgqgtlvt
vssas

  • Chain 'L':
    Sequence, based on SEQRES records:
    >7k8tL (L:)
diqltqspsslsasvgdrvtitcrasqsissylnwyqqkpgkapklliyaasslqsgvps
rfsgsgsgtdftltisslqpedfatyycqqsystprtfgqgtkveikrtvaapsvfifpp
sdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstlt
lskadyekhkvyacevthqglsspvtksfnrgec

    Sequence, based on observed residues (ATOM records):
    >7k8tL (L:)
diqltqspsslsasvgdrvtitcrasqsissylnwyqqkpgkapklliyaasslqsgvps
rfsgsgsgtdftltisslqpedfatyycqqsystprtfgqgtkveik

  • Chain 'M':
    Sequence, based on SEQRES records:
    >7k8tM (M:)
evqlvesgggvvqpgrslrlscaasgftfsiygmhwvrqapgkglewvavisydgsnkyy
adsvkgrftisrdnskntlylqmnslraedtavyycakegrpsdivvvvafdywgqgtlv
tvssastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpav
lqssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkrvepkscdkthhhhhh

    Sequence, based on observed residues (ATOM records):
    >7k8tM (M:)
vqlvesgggvvqpgrslrlscaasgftfsiygmhwvrqapgkglewvavisydgsnkyya
dsvkgrftisrdnskntlylqmnslraedtavyycakegrpsdivvvvafdywgqgtlvt
vssas

  • Chain 'N':
    Sequence, based on SEQRES records:
    >7k8tN (N:)
diqltqspsslsasvgdrvtitcrasqsissylnwyqqkpgkapklliyaasslqsgvps
rfsgsgsgtdftltisslqpedfatyycqqsystprtfgqgtkveikrtvaapsvfifpp
sdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstlt
lskadyekhkvyacevthqglsspvtksfnrgec

    Sequence, based on observed residues (ATOM records):
    >7k8tN (N:)
diqltqspsslsasvgdrvtitcrasqsissylnwyqqkpgkapklliyaasslqsgvps
rfsgsgsgtdftltisslqpedfatyycqqsystprtfgqgtkveik

  • Chain 'O':
    Sequence, based on SEQRES records:
    >7k8tO (O:)
evqlvesgggvvqpgrslrlscaasgftfsiygmhwvrqapgkglewvavisydgsnkyy
adsvkgrftisrdnskntlylqmnslraedtavyycakegrpsdivvvvafdywgqgtlv
tvssastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpav
lqssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkrvepkscdkthhhhhh

    Sequence, based on observed residues (ATOM records):
    >7k8tO (O:)
vqlvesgggvvqpgrslrlscaasgftfsiygmhwvrqapgkglewvavisydgsnkyya
dsvkgrftisrdnskntlylqmnslraedtavyycakegrpsdivvvvafdywgqgtlvt
vssas

  • Chain 'P':
    Sequence, based on SEQRES records:
    >7k8tP (P:)
diqltqspsslsasvgdrvtitcrasqsissylnwyqqkpgkapklliyaasslqsgvps
rfsgsgsgtdftltisslqpedfatyycqqsystprtfgqgtkveikrtvaapsvfifpp
sdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstlt
lskadyekhkvyacevthqglsspvtksfnrgec

    Sequence, based on observed residues (ATOM records):
    >7k8tP (P:)
diqltqspsslsasvgdrvtitcrasqsissylnwyqqkpgkapklliyaasslqsgvps
rfsgsgsgtdftltisslqpedfatyycqqsystprtfgqgtkveik