PDB entry 6z43

View 6z43 on RCSB PDB site
Description: cryo-em structure of sars-cov-2 spike : h11-d4 nanobody complex
Deposited on 2020-05-22, released 2020-06-03
The last revision was dated 2020-07-29, with a file datestamp of 2020-06-29.
Experiment type: EM
Resolution: 3.3 Å
R-factor: N/A
AEROSPACI score: 0.2 (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 'X':
    Compound: Nanobody
    Species: LAMA GLAMA [TaxId:9844]
    Database cross-references and differences (RAF-indexed):
    • PDB 6Z43 (0-End)
  • Chain 'Y':
    Compound: Nanobody
    Species: LAMA GLAMA [TaxId:9844]
    Database cross-references and differences (RAF-indexed):
    • PDB 6Z43 (0-End)
  • Chain 'Z':
    Compound: Nanobody
    Species: LAMA GLAMA [TaxId:9844]
    Database cross-references and differences (RAF-indexed):
    • PDB 6Z43 (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:
    >6z43A (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):
    >6z43A (A:)
aytnsftrgvyypdkvfrssvlhstqdlflpffsnvtwfhnpvlpfndgvyfasteksni
irgwifgttldsktqsllivnnatnvvikvcefqfcndpfnnctfeyvsfknlrefvfkn
yfkiyskhtpindlpqgfsaleplvdlpiginitrfqtllaayyvgylqprtfllkynen
gtitdavdcaldplsetkctlksftvekgiyqtsnfrvqptesivrfpnitnlcpfgevf
natrfasvyawnrkrisncvadysvlynsasfstfkcygvsptklndlcftnvyadsfvi
rgdevrqiapgqtgkiadynyklpddftgcviawnsnnldskvggnynylyrlfrksnlk
pferdisteiyqagstpcngvegfncyfplqsygfqptngvgyqpyrvvvlsfellhapa
tvcgpkkstnlvknkcvnfnfngltgtgvltesnkkflpfqqfgrdiadttdavrdpqtl
eilditpcsfggvsvitpgtntsnqvavlyqdvnctevnvfqtragcligaehvnnsyec
dipigagicasyqtsqsiiaytmslgaensvaysnnsiaiptnftisvtteilpvsmtkt
svdctmyicgdstecsnlllqygsfctqlnraltgiaveqdkntqevfaqvkqiyktppi
kdfggfnfsqilpdpskpskrsfiedllfnkvtkfngltvlpplltdemiaqytsallag
titsgwtfgagaalqipfamqmayrfngigvtqnvlyenqklianqfnsaigkiqdslss
tasalgklqdvvnqnaqalntlvkqlssnfgaissvlndilsrldppeaevqidrlitgr
lqslqtyvtqqliraaeirasanlaatkmsecvlgqskrvdfcgkgyhlmsfpqsaphgv
vflhvtyvpaqeknfttapaichdgkahfpregvfvsngthwfvtqrnfyepqiittdnt
fvsgncdvvigivnntvydplqpelds

  • Chain 'B':
    Sequence, based on SEQRES records:
    >6z43B (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):
    >6z43B (B:)
aytnsftrgvyypdkvfrssvlhstqdlflpffsnvtwfhaihpvlpfndgvyfasteks
niirgwifgttldsksllivnnatnvvikvcefqfcndpflgvctfeyvsfknlrefvfk
nidgyfkiyskhtpinlvrdlpqgfsaleplvdlpiginitrfqtllaayyvgylqprtf
llkynengtitdavdcaldplsetkctlksftvekgiyqtsnfrvqptesivrfpnitnl
cpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygvsptklndlcftnv
yadsfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnldskvggnynylyrl
frksnlkpferdisteiyqagstpcngvegfncyfplqsygfqptngvgyqpyrvvvlsf
ellhapatvcgpkkstnlvknkcvnfnfngltgtgvltesnkkflpfqqfgrdiadttda
vrdpqtleilditpcsfggvsvitpgtntsnqvavlyqdvnctevnvfqtragcligaeh
vnnsyecdipigagicasyqtqsiiaytmslgaensvaysnnsiaiptnftisvtteilp
vsmtktsvdctmyicgdstecsnlllqygsfctqlnraltgiaveqdkntqevfaqvkqi
yktppikdfggfnfsqilpdpskpskrsfiedllfnkvtfngltvlpplltdemiaqyts
allagtitsgwtfgagaalqipfamqmayrfngigvtqnvlyenqklianqfnsaigkiq
dslsstasalgklqdvvnqnaqalntlvkqlssnfgaissvlndilsrldppeaevqidr
litgrlqslqtyvtqqliraaeirasanlaatkmsecvlgqskrvdfcgkgyhlmsfpqs
aphgvvflhvtyvpaqeknfttapaichdgkahfpregvfvsngthwfvtqrnfyepqii
ttdntfvsgncdvvigivnntvydplqpelds

  • Chain 'C':
    Sequence, based on SEQRES records:
    >6z43C (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):
    >6z43C (C:)
aytnsftrgvyypdkvfrssvlhstqdlflpffsnvtwfhnpvlpfndgvyfasteksni
irgwifgttldsktqsllivnnatnvvikvcefqfcndpflgvnctfeyvsfknlrefvf
knidgyfkiyskhtpinlvrdlpqgfsaleplvdlpiginitrfqtllayyvgylqprtf
llkynengtitdavdcaldplsetkctlksftvekgiyqtsnfrvqptesivrfpnitnl
cpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygvsptklndlcftnv
yadsfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnldskvggnynylyrl
frksnlkpferdisteiyqagstpcngvegfncyfplqsygfqptngvgyqpyrvvvlsf
ellhapatvcgpkkstnlvknkcvnfnfngltgtgvltesnkkflpfqqfgrdiadttda
vrdpqtleilditpcsfggvsvitpgtntsnqvavlyqdvnctevnvfqtragcligaeh
vnnsyecdipigagicasyqtqsiiaytmslgaensvaysnnsiaiptnftisvtteilp
vsmtktsvdctmyicgdstecsnlllqygsfctqlnraltgiaveqdkntqevfaqvkqi
yktppikdfggfnfsqilpdpskpskrsfiedllfnkvtngltvlpplltdemiaqytsa
llagtitsgwtfgagaalqipfamqmayrfngigvtqnvlyenqklianqfnsaigkiqd
slsstasalgklqdvvnqnaqalntlvkqlssnfgaissvlndilsrldppeaevqidrl
itgrlqslqtyvtqqliraaeirasanlaatkmsecvlgqskrvdfcgkgyhlmsfpqsa
phgvvflhvtyvpaqeknfttapaichdgkahfpregvfvsngthwfvtqrnfyepqiit
tdntfvsgncdvvigivnntvydplqpelds

  • Chain 'X':
    Sequence, based on SEQRES records:
    >6z43X (X:)
qvqlvesggglmqaggslrlscavsgrtfstaamgwfrqapgkerefvaairwsggsayy
adsvkgrftisrdkakntvylqmnslkyedtavyycartenvrsllsdyatwpydywgqg
tqvtvssgpggqhhhhhhgaeqkliseedls

    Sequence, based on observed residues (ATOM records):
    >6z43X (X:)
qvqlvesggglmqaggslrlscavsgrtfstaamgwfrqapgkerefvaairwsggsayy
adsvkgrftisrdkakntvylqmnslkyedtavyycartenvrsllsdyatwpydywgqg
tqvtvss

  • Chain 'Y':
    Sequence, based on SEQRES records:
    >6z43Y (Y:)
qvqlvesggglmqaggslrlscavsgrtfstaamgwfrqapgkerefvaairwsggsayy
adsvkgrftisrdkakntvylqmnslkyedtavyycartenvrsllsdyatwpydywgqg
tqvtvssgpggqhhhhhhgaeqkliseedls

    Sequence, based on observed residues (ATOM records):
    >6z43Y (Y:)
qvqlvesggglmqaggslrlscavsgrtfstaamgwfrqapgkerefvaairwsggsayy
adsvkgrftisrdkakntvylqmnslkyedtavyycartenvrsllsdyatwpydywgqg
tqvtvss

  • Chain 'Z':
    Sequence, based on SEQRES records:
    >6z43Z (Z:)
qvqlvesggglmqaggslrlscavsgrtfstaamgwfrqapgkerefvaairwsggsayy
adsvkgrftisrdkakntvylqmnslkyedtavyycartenvrsllsdyatwpydywgqg
tqvtvssgpggqhhhhhhgaeqkliseedls

    Sequence, based on observed residues (ATOM records):
    >6z43Z (Z:)
qvqlvesggglmqaggslrlscavsgrtfstaamgwfrqapgkerefvaairwsggsayy
adsvkgrftisrdkakntvylqmnslkyedtavyycartenvrsllsdyatwpydywgqg
tqvtvss