PDB entry 7ksg

View 7ksg on RCSB PDB site
Description: sars-cov-2 spike in complex with nanobodies e
Deposited on 2020-11-22, released 2021-01-20
The last revision was dated 2021-06-30, with a file datestamp of 2021-06-25.
Experiment type: EM
Resolution: 3.33 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
      • 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 'D':
    Compound: Nanobody against SARS-CoV-2 glycoprotein
    Species: Lama glama [TaxId:9844]
    Database cross-references and differences (RAF-indexed):
    • PDB 7KSG (0-End)
  • Chain 'E':
    Compound: Nanobody against SARS-CoV-2 glycoprotein
    Species: Lama glama [TaxId:9844]
    Database cross-references and differences (RAF-indexed):
    • PDB 7KSG (0-End)
  • Chain 'F':
    Compound: Nanobody against SARS-CoV-2 glycoprotein
    Species: Lama glama [TaxId:9844]
    Database cross-references and differences (RAF-indexed):
    • PDB 7KSG (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:
    >7ksgA (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):
    >7ksgA (A:)
qlppaytnsftrgvyypdkvfrssvlhstqdlflpffsnvtwfhaihvtkrfdnpvlpfn
dgvyfasteksniirgwifgttldsktqsllivnnatnvvikvcefqfcndpflgvyyhk
nnkswmesefrvyssannctfeyvsqpflmdlegkqgnfknlrefvfknidgyfkiyskh
tpinlvrdlpqgfsaleplvdlpiginitrfqtllalhrsgdsssgwtagaaayyvgylq
prtfllkynengtitdavdcaldplsetkctlksftvekgiyqtsnfrvqptesivrfpn
itnlcpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygvsptklndlc
ftnvyadsfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnldskvggnyny
lyrlfrksnlkpferdisteiyqagstpcngvegfncyfplqsygfqptngvgyqpyrvv
vlsfellhapatvcgpkkstnlvknkcvnfnfngltgtgvltesnkkflpfqqfgrdiad
ttdavrdpqtleilditpcsfggvsvitpgtntsnqvavlyqdvnctevnvfqtragcli
gaehvnnsyecdipigagicasysiiaytmslgaensvaysnnsiaiptnftisvtteil
pvsmtktsvdctmyicgdstecsnlllqygsfctqlnraltgiaveqdkntqevfaqvkq
iyktppikdfggfnfsqilpdpskpskrsfiedllfnkvtlfngltvlpplltdemiaqy
tsallagtitsgwtfgagaalqipfamqmayrfngigvtqnvlyenqklianqfnsaigk
iqdslsstasalgklqdvvnqnaqalntlvkqlssnfgaissvlndilsrldppeaevqi
drlitgrlqslqtyvtqqliraaeirasanlaatkmsecvlgqskrvdfcgkgyhlmsfp
qsaphgvvflhvtyvpaqeknfttapaichdgkahfpregvfvsngthwfvtqrnfyepq
iittdntfvsgncdvvigivnntvydplqpeld

  • Chain 'B':
    Sequence, based on SEQRES records:
    >7ksgB (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):
    >7ksgB (B:)
qcvnlttrtqlppaytnsftrgvyypdkvfrssvlhstqdlflpffsnvtwfhaihvtkr
fdnpvlpfndgvyfasteksniirgwifgttldsktqsllivnnatnvvikvcefqfcnd
pflgvyyhknnkswmesefrvyssannctfeyvsqpflmdlegkqgnfknlrefvfknid
gyfkiyskhtpinlvrdlpqgfsaleplvdlpiginitrfqtllalhrsgdsssgwtaga
aayyvgylqprtfllkynengtitdavdcaldplsetkctlksftvekgiyqtsnfrvqp
tesivrfpnitnlcpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygv
sptklndlcftnvyadsfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnld
skvggnynylyrlfrksnlkpferdisteiyqagstpcngvegfncyfplqsygfqptng
vgyqpyrvvvlsfellhapatvcgpkkstnlvknkcvnfnfngltgtgvltesnkkflpf
qqfgrdiadttdavrdpqtleilditpcsfggvsvitpgtntsnqvavlyqdvnctevnv
fqtragcligaehvnnsyecdipigagicasysiiaytmslgaensvaysnnsiaiptnf
tisvtteilpvsmtktsvdctmyicgdstecsnlllqygsfctqlnraltgiaveqdknt
qevfaqvkqiyktppikdfggfnfsqilpdpskpskrsfiedllfnkvtlfngltvlppl
ltdemiaqytsallagtitsgwtfgagaalqipfamqmayrfngigvtqnvlyenqklia
nqfnsaigkiqdslsstasalgklqdvvnqnaqalntlvkqlssnfgaissvlndilsrl
dppeaevqidrlitgrlqslqtyvtqqliraaeirasanlaatkmsecvlgqskrvdfcg
kgyhlmsfpqsaphgvvflhvtyvpaqeknfttapaichdgkahfpregvfvsngthwfv
tqrnfyepqiittdntfvsgncdvvigivnntvydplqpeld

  • Chain 'C':
    Sequence, based on SEQRES records:
    >7ksgC (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):
    >7ksgC (C:)
qcvnlttrtqlppaytnsftrgvyypdkvfrssvlhstqdlflpffsnvtwfhaihvtkr
fdnpvlpfndgvyfasteksniirgwifgttldsktqsllivnnatnvvikvcefqfcnd
pflgvyyhknnkswmesefrvyssannctfeyvsqpflmdlegkqgnfknlrefvfknid
gyfkiyskhtpinlvrdlpqgfsaleplvdlpiginitrfqtllalhrsgdsssgwtaga
aayyvgylqprtfllkynengtitdavdcaldplsetkctlksftvekgiyqtsnfrvqp
tesivrfpnitnlcpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygv
sptklndlcftnvyadsfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnld
skvggnynylyrlfrksnlkpferdisteiyqagstpcngvegfncyfplqsygfqptng
vgyqpyrvvvlsfellhapatvcgpkkstnlvknkcvnfnfngltgtgvltesnkkflpf
qqfgrdiadttdavrilditpcsfggvsvitpgtntsnqvavlyqdvnctevnvfqtrag
cligaehvnnsyecdipigagicasysiiaytmslgaensvaysnnsiaiptnftisvtt
eilpvsmtktsvdctmyicgdstecsnlllqygsfctqlnraltgiaveqdkntqevfaq
vkqiyktppikdfggfnfsqilpdpskpskrsfiedllfnkvtlfngltvlpplltdemi
aqytsallagtitsgwtfgagaalqipfamqmayrfngigvtqnvlyenqklianqfnsa
igkiqdslsstasalgklqdvvnqnaqalntlvkqlssnfgaissvlndilsrldppeae
vqidrlitgrlqslqtyvtqqliraaeirasanlaatkmsecvlgqskrvdfcgkgyhlm
sfpqsaphgvvflhvtyvpaqeknfttapaichdgkahfpregvfvsngthwfvtqrnfy
epqiittdntfvsgncdvvigivnntvydplqpeld

  • Chain 'D':
    Sequence, based on SEQRES records:
    >7ksgD (D:)
qvqlvetgggfvqpggslrlscaasgvtldyyaigwfrqapgkeregvscigssdgrtyy
sdsvkgrftisrdnakntvylqmnslkpedtavyycaltvgtyysgnyhytcsddmdywg
kgtqvtvssgglpetgghhhhhh

    Sequence, based on observed residues (ATOM records):
    >7ksgD (D:)
qvqlvetgggfvqpggslrlscaasgvtldyyaigwfrqapgkeregvscigssdgrtyy
sdsvkgrftisrdnakntvylqmnslkpedtavyycaltvgtyysgnyhytcsddmdywg
kgtqvtvss

  • Chain 'E':
    Sequence, based on SEQRES records:
    >7ksgE (E:)
qvqlvetgggfvqpggslrlscaasgvtldyyaigwfrqapgkeregvscigssdgrtyy
sdsvkgrftisrdnakntvylqmnslkpedtavyycaltvgtyysgnyhytcsddmdywg
kgtqvtvssgglpetgghhhhhh

    Sequence, based on observed residues (ATOM records):
    >7ksgE (E:)
qvqlvetgggfvqpggslrlscaasgvtldyyaigwfrqapgkeregvscigssdgrtyy
sdsvkgrftisrdnakntvylqmnslkpedtavyycaltvgtyysgnyhytcsddmdywg
kgtqvtvss

  • Chain 'F':
    Sequence, based on SEQRES records:
    >7ksgF (F:)
qvqlvetgggfvqpggslrlscaasgvtldyyaigwfrqapgkeregvscigssdgrtyy
sdsvkgrftisrdnakntvylqmnslkpedtavyycaltvgtyysgnyhytcsddmdywg
kgtqvtvssgglpetgghhhhhh

    Sequence, based on observed residues (ATOM records):
    >7ksgF (F:)
qvqlvetgggfvqpggslrlscaasgvtldyyaigwfrqapgkeregvscigssdgrtyy
sdsvkgrftisrdnakntvylqmnslkpedtavyycaltvgtyysgnyhytcsddmdywg
kgtqvtvss