PDB entry 7kkk

View 7kkk on RCSB PDB site
Description: sars-cov-2 spike in complex with neutralizing nanobody nb6
Deposited on 2020-10-27, released 2020-11-11
The last revision was dated 2021-04-21, with a file datestamp of 2021-04-16.
Experiment type: EM
Resolution: 3.03 Å
R-factor: N/A
AEROSPACI score: 0.26 (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: Synthetic nanobody Nb6
    Species: synthetic construct, synthetic [TaxId:32630]
    Database cross-references and differences (RAF-indexed):
    • PDB 7KKK (Start-118)
  • 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: Synthetic nanobody Nb6
    Species: synthetic construct, synthetic [TaxId:32630]
    Database cross-references and differences (RAF-indexed):
    • PDB 7KKK (Start-118)
  • Chain 'E':
    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 'F':
    Compound: Synthetic nanobody Nb6
    Species: synthetic construct, synthetic [TaxId:32630]
    Database cross-references and differences (RAF-indexed):
    • PDB 7KKK (Start-118)
  • 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:
    >7kkkA (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):
    >7kkkA (A:)
aytnsftrgvyypdkvfrssvlhstqdlflpffsnvtwfhaihdnpvlpfndgvyfaste
ksniirgwifgttldsktqsllivnnatnvvikvcefqfcndpflgvnctfeyvsfknlr
efvfknidgyfkiyskhtpinlvrdlpqgfsaleplvdlpiginitrfqtllalhaayyv
gylqprtfllkynengtitdavdcaldplsetkctlksftvekgiyqtsnfrvqptesiv
rfpnitnlcpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygvsptkl
ndlcftnvyadsfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnldskvgg
nynylyrlfrksnlkpferdisteiyqagstpcngvegfncyfplqsygfqptngvgyqp
yrvvvlsfellhapatvcgpkkstnlvknkcvnfnfngltgtgvltesnkkflpfqqfgr
diadttdavrdpqtleilditpcsfggvsvitpgtntsnqvavlyqdvnctevnvfqtra
gcligaehvnnsyecdipigagicasyqtsqsiiaytmslgaensvaysnnsiaiptnft
isvtteilpvsmtktsvdctmyicgdstecsnlllqygsfctqlnraltgiaveqdkntq
evfaqvkqiyktppikdfggfnfsqilpdpskpskrsfiedllfnkvtkfngltvlppll
tdemiaqytsallagtitsgwtfgagaalqipfamqmayrfngigvtqnvlyenqklian
qfnsaigkiqdslsstasalgklqdvvnqnaqalntlvkqlssnfgaissvlndilsrld
ppeaevqidrlitgrlqslqtyvtqqliraaeirasanlaatkmsecvlgqskrvdfcgk
gyhlmsfpqsaphgvvflhvtyvpaqeknfttapaichdgkahfpregvfvsngthwfvt
qrnfyepqiittdntfvsgncdvvigivnntvydplqpelds

  • Chain 'B':
    Sequence, based on SEQRES records:
    >7kkkB (B:)
qvqlvesggglvqaggslrlscaasgiifgrnamgwyrqapgkerelvagitrrgsityy
adsvkgrftisrdnakntvylqmnslkpedtavyycaadpaspapgdywgqgtqvtvss

    Sequence, based on observed residues (ATOM records):
    >7kkkB (B:)
vqlvesggglvqaggslrlscaasgiifgrnamgwyrqapgkerelvagitrrgsityya
dsvkgrftisrdnakntvylqmnslkpedtavyycaadpaspapgdywgqgtqvtvss

  • Chain 'C':
    Sequence, based on SEQRES records:
    >7kkkC (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):
    >7kkkC (C:)
aytnsftrgvyypdkvfrssvlhstqdlflpffsnvtwfhaihdnpvlpfndgvyfaste
ksniirgwifgttldsktqsllivnnatnvvikvcefqfcndpflgvnctfeyvsfknlr
efvfknidgyfkiyskhtpinlvrdlpqgfsaleplvdlpiginitrfqtllalhaayyv
gylqprtfllkynengtitdavdcaldplsetkctlksftvekgiyqtsnfrvqptesiv
rfpnitnlcpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygvsptkl
ndlcftnvyadsfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnldskvgg
nynylyrlfrksnlkpferdisteiyqagstpcngvegfncyfplqsygfqptngvgyqp
yrvvvlsfellhapatvcgpkkstnlvknkcvnfnfngltgtgvltesnkkflpfqqfgr
diadttdavrdpqtleilditpcsfggvsvitpgtntsnqvavlyqdvnctevnvfqtra
gcligaehvnnsyecdipigagicasyqtsqsiiaytmslgaensvaysnnsiaiptnft
isvtteilpvsmtktsvdctmyicgdstecsnlllqygsfctqlnraltgiaveqdkntq
evfaqvkqiyktppikdfggfnfsqilpdpskpskrsfiedllfnkvtkfngltvlppll
tdemiaqytsallagtitsgwtfgagaalqipfamqmayrfngigvtqnvlyenqklian
qfnsaigkiqdslsstasalgklqdvvnqnaqalntlvkqlssnfgaissvlndilsrld
ppeaevqidrlitgrlqslqtyvtqqliraaeirasanlaatkmsecvlgqskrvdfcgk
gyhlmsfpqsaphgvvflhvtyvpaqeknfttapaichdgkahfpregvfvsngthwfvt
qrnfyepqiittdntfvsgncdvvigivnntvydplqpelds

  • Chain 'D':
    Sequence, based on SEQRES records:
    >7kkkD (D:)
qvqlvesggglvqaggslrlscaasgiifgrnamgwyrqapgkerelvagitrrgsityy
adsvkgrftisrdnakntvylqmnslkpedtavyycaadpaspapgdywgqgtqvtvss

    Sequence, based on observed residues (ATOM records):
    >7kkkD (D:)
vqlvesggglvqaggslrlscaasgiifgrnamgwyrqapgkerelvagitrrgsityya
dsvkgrftisrdnakntvylqmnslkpedtavyycaadpaspapgdywgqgtqvtvss

  • Chain 'E':
    Sequence, based on SEQRES records:
    >7kkkE (E:)
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):
    >7kkkE (E:)
aytnsftrgvyypdkvfrssvlhstqdlflpffsnvtwfhaihdnpvlpfndgvyfaste
ksniirgwifgttldsktqsllivnnatnvvikvcefqfcndpflgvnctfeyvsfknlr
efvfknidgyfkiyskhtpinlvrdlpqgfsaleplvdlpiginitrfqtllalhaayyv
gylqprtfllkynengtitdavdcaldplsetkctlksftvekgiyqtsnfrvqptesiv
rfpnitnlcpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygvsptkl
ndlcftnvyadsfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnldskvgg
nynylyrlfrksnlkpferdisteiyqagstpcngvegfncyfplqsygfqptngvgyqp
yrvvvlsfellhapatvcgpkkstnlvknkcvnfnfngltgtgvltesnkkflpfqqfgr
diadttdavrdpqtleilditpcsfggvsvitpgtntsnqvavlyqdvnctevnvfqtra
gcligaehvnnsyecdipigagicasyqtsqsiiaytmslgaensvaysnnsiaiptnft
isvtteilpvsmtktsvdctmyicgdstecsnlllqygsfctqlnraltgiaveqdkntq
evfaqvkqiyktppikdfggfnfsqilpdpskpskrsfiedllfnkvtkfngltvlppll
tdemiaqytsallagtitsgwtfgagaalqipfamqmayrfngigvtqnvlyenqklian
qfnsaigkiqdslsstasalgklqdvvnqnaqalntlvkqlssnfgaissvlndilsrld
ppeaevqidrlitgrlqslqtyvtqqliraaeirasanlaatkmsecvlgqskrvdfcgk
gyhlmsfpqsaphgvvflhvtyvpaqeknfttapaichdgkahfpregvfvsngthwfvt
qrnfyepqiittdntfvsgncdvvigivnntvydplqpelds

  • Chain 'F':
    Sequence, based on SEQRES records:
    >7kkkF (F:)
qvqlvesggglvqaggslrlscaasgiifgrnamgwyrqapgkerelvagitrrgsityy
adsvkgrftisrdnakntvylqmnslkpedtavyycaadpaspapgdywgqgtqvtvss

    Sequence, based on observed residues (ATOM records):
    >7kkkF (F:)
vqlvesggglvqaggslrlscaasgiifgrnamgwyrqapgkerelvagitrrgsityya
dsvkgrftisrdnakntvylqmnslkpedtavyycaadpaspapgdywgqgtqvtvss