PDB entry 7ndd

View 7ndd on RCSB PDB site
Description: em structure of sars-cov-2 spike glycoprotein (one rbd up) in complex with covox-159
Deposited on 2021-01-30, released 2021-03-03
The last revision was dated 2021-04-28, with a file datestamp of 2021-04-23.
Experiment type: EM
Resolution: 4.2 Å
R-factor: N/A
AEROSPACI score: 0.13 (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: COVOX-159 Fab heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7NDD
  • Chain 'E':
    Compound: COVOX-159 Fab light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7NDD
  • Chain 'F':
    Compound: COVOX-159 Fab heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7NDD
  • Chain 'G':
    Compound: COVOX-159 Fab light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7NDD
  • Chain 'H':
    Compound: COVOX-159 Fab heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7NDD
  • Chain 'L':
    Compound: COVOX-159 Fab light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7NDD
  • 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:
    >7nddA (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):
    >7nddA (A:)
qcvnlttrtqlppaytnsftrgvyypdkvfrssvlhstqdlflpffsnvtwfhaihkrfd
npvlpfndgvyfasteksniirgwifgttldsktqsllivnnatnvvikvcefqfcndpf
lgvyyhknnkswmesefrvyssannctfeyvsqpflmdnfknlrefvfknidgyfkiysk
htpinlvrdlpqgfsaleplvdlpiginitrfqtllalhrsyltpgdsssgwtagaaayy
vgylqprtfllkynengtitdavdcaldplsetkctlksftvekgiyqtsnfrvqptesi
vrfpnitnlcpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygvsptk
lndlcftnvyadsfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnldskvg
gnynylyrlfrksnlkpferdisteiyqagstpcngvegfncyfplqsygfqptngvgyq
pyrvvvlsfellhapatvcgpkkstnlvknkcvnfnfngltgtgvltesnkkflpfqqfg
rdiadttdavrdpqtleilditpcsfggvsvitpgtntsnqvavlyqdvnctevnvfqtr
agcligaehvnnsyecdipigagicasyqtsqsiiaytmslgaensvaysnnsiaiptnf
tisvtteilpvsmtktsvdctmyicgdstecsnlllqygsfctqlnraltgiaveqdknt
qevfaqvkqiyktppikdfggfnfsqilpdpskpskrsfiedllfnkvtkfngltvlppl
ltdemiaqytsallagtitsgwtfgagaalqipfamqmayrfngigvtqnvlyenqklia
nqfnsaigkiqdslsstasalgklqdvvnqnaqalntlvkqlssnfgaissvlndilsrl
dppeaevqidrlitgrlqslqtyvtqqliraaeirasanlaatkmsecvlgqskrvdfcg
kgyhlmsfpqsaphgvvflhvtyvpaqeknfttapaichdgkahfpregvfvsngthwfv
tqrnfyepqiittdntfvsgncdvvigivnntvydplqpelds

  • Chain 'B':
    Sequence, based on SEQRES records:
    >7nddB (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):
    >7nddB (B:)
qcvnlttrtqlppaytnsftrgvyypdkvfrssvlhstqdlflpffsnvtwfhaihkrfd
npvlpfndgvyfasteksniirgwifgttldsktqsllivnnatnvvikvcefqfcndpf
lgvyyhknnkswmesefrvyssannctfeyvsqpflmdnfknlrefvfknidgyfkiysk
htpinlvrdlpqgfsaleplvdlpiginitrfqtllalhrsyltpgdsssgwtagaaayy
vgylqprtfllkynengtitdavdcaldplsetkctlksftvekgiyqtsnfrvqptesi
vrfpnitnlcpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygvsptk
lndlcftnvyadsfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnldskvg
gnynylyrlfrksnlkpferdisteiyqagstpcngvegfncyfplqsygfqptngvgyq
pyrvvvlsfellhapatvcgpkkstnlvknkcvnfnfngltgtgvltesnkkflpfqqfg
rdiadttdavrdpqtleilditpcsfggvsvitpgtntsnqvavlyqdvnctevnvfqtr
agcligaehvnnsyecdipigagicasyqtsqsiiaytmslgaensvaysnnsiaiptnf
tisvtteilpvsmtktsvdctmyicgdstecsnlllqygsfctqlnraltgiaveqdknt
qevfaqvkqiyktppikdfggfnfsqilpdpskpskrsfiedllfnkvtkfngltvlppl
ltdemiaqytsallagtitsgwtfgagaalqipfamqmayrfngigvtqnvlyenqklia
nqfnsaigkiqdslsstasalgklqdvvnqnaqalntlvkqlssnfgaissvlndilsrl
dppeaevqidrlitgrlqslqtyvtqqliraaeirasanlaatkmsecvlgqskrvdfcg
kgyhlmsfpqsaphgvvflhvtyvpaqeknfttapaichdgkahfpregvfvsngthwfv
tqrnfyepqiittdntfvsgncdvvigivnntvydplqpelds

  • Chain 'C':
    Sequence, based on SEQRES records:
    >7nddC (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):
    >7nddC (C:)
qcvnlttrtqlppaytnsftrgvyypdkvfrssvlhstqdlflpffsnvtwfhaihkrfd
npvlpfndgvyfasteksniirgwifgttldsktqsllivnnatnvvikvcefqfcndpf
lgvyyhknnkswmesefrvyssannctfeyvsqpflmdnfknlrefvfknidgyfkiysk
htpinlvrdlpqgfsaleplvdlpiginitrfqtllalhrsyltpgdsssgwtagaaayy
vgylqprtfllkynengtitdavdcaldplsetkctlksftvekgiyqtsnfrvqptesi
vrfpnitnlcpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygvsptk
lndlcftnvyadsfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnldskvg
gnynylyrlfrksnlkpferdisteiyqagstpcngvegfncyfplqsygfqptngvgyq
pyrvvvlsfellhapatvcgpkkstnlvknkcvnfnfngltgtgvltesnkkflpfqqfg
rdiadttdavrdpqtleilditpcsfggvsvitpgtntsnqvavlyqdvnctevnvfqtr
agcligaehvnnsyecdipigagicasyqtsqsiiaytmslgaensvaysnnsiaiptnf
tisvtteilpvsmtktsvdctmyicgdstecsnlllqygsfctqlnraltgiaveqdknt
qevfaqvkqiyktppikdfggfnfsqilpdpskpskrsfiedllfnkvtkfngltvlppl
ltdemiaqytsallagtitsgwtfgagaalqipfamqmayrfngigvtqnvlyenqklia
nqfnsaigkiqdslsstasalgklqdvvnqnaqalntlvkqlssnfgaissvlndilsrl
dppeaevqidrlitgrlqslqtyvtqqliraaeirasanlaatkmsecvlgqskrvdfcg
kgyhlmsfpqsaphgvvflhvtyvpaqeknfttapaichdgkahfpregvfvsngthwfv
tqrnfyepqiittdntfvsgncdvvigivnntvydplqpelds

  • Chain 'D':
    Sequence, based on SEQRES records:
    >7nddD (D:)
ilflvatatgvhsevqlvesgggvvqpgrslrlscaasgftfssygmhwvrqapgkglew
valisydggnryyadsvkgrftisrdnskntlylqmnrlraedtamyycakdrddgwdwy
yfmdvwgkgttvtvssastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsg
altsgvhtfpavlqssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepkscd
k

    Sequence, based on observed residues (ATOM records):
    >7nddD (D:)
vqlvesgggvvqpgrslrlscaasgftfssygmhwvrqapgkglewvalisydggnryya
dsvkgrftisrdnskntlylqmnrlraedtamyycakdryfmdvwgkgttvtvss

  • Chain 'E':
    Sequence, based on SEQRES records:
    >7nddE (E:)
ilflvatatgvhsdiqltqspgtlslspgeratlscrasqsisgnylawyqhkpgqaprl
liygastratgipdrfsgsgsgtdftltisrlepedfavyycqqygssytfgqgtkveik
rtvaapsvfifppsdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqd
skdstyslsstltlskadyekhkvyacevthqglsspvtksfnrgec

    Sequence, based on observed residues (ATOM records):
    >7nddE (E:)
iqltqspgtlslspgeratlscrasqsisgnylawyqhkpgqaprlliygastratgipd
rfsgsgsgtdftltisrlepedfavyycqqygssytfgqgtkveik

  • Chain 'F':
    Sequence, based on SEQRES records:
    >7nddF (F:)
ilflvatatgvhsevqlvesgggvvqpgrslrlscaasgftfssygmhwvrqapgkglew
valisydggnryyadsvkgrftisrdnskntlylqmnrlraedtamyycakdrddgwdwy
yfmdvwgkgttvtvssastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsg
altsgvhtfpavlqssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepkscd
k

    Sequence, based on observed residues (ATOM records):
    >7nddF (F:)
vqlvesgggvvqpgrslrlscaasgftfssygmhwvrqapgkglewvalisydggnryya
dsvkgrftisrdnskntlylqmnrlraedtamyycakdryfmdvwgkgttvtvss

  • Chain 'G':
    Sequence, based on SEQRES records:
    >7nddG (G:)
ilflvatatgvhsdiqltqspgtlslspgeratlscrasqsisgnylawyqhkpgqaprl
liygastratgipdrfsgsgsgtdftltisrlepedfavyycqqygssytfgqgtkveik
rtvaapsvfifppsdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqd
skdstyslsstltlskadyekhkvyacevthqglsspvtksfnrgec

    Sequence, based on observed residues (ATOM records):
    >7nddG (G:)
iqltqspgtlslspgeratlscrasqsisgnylawyqhkpgqaprlliygastratgipd
rfsgsgsgtdftltisrlepedfavyycqqygssytfgqgtkveik

  • Chain 'H':
    Sequence, based on SEQRES records:
    >7nddH (H:)
ilflvatatgvhsevqlvesgggvvqpgrslrlscaasgftfssygmhwvrqapgkglew
valisydggnryyadsvkgrftisrdnskntlylqmnrlraedtamyycakdrddgwdwy
yfmdvwgkgttvtvssastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsg
altsgvhtfpavlqssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepkscd
k

    Sequence, based on observed residues (ATOM records):
    >7nddH (H:)
vqlvesgggvvqpgrslrlscaasgftfssygmhwvrqapgkglewvalisydggnryya
dsvkgrftisrdnskntlylqmnrlraedtamyycakdryfmdvwgkgttvtvss

  • Chain 'L':
    Sequence, based on SEQRES records:
    >7nddL (L:)
ilflvatatgvhsdiqltqspgtlslspgeratlscrasqsisgnylawyqhkpgqaprl
liygastratgipdrfsgsgsgtdftltisrlepedfavyycqqygssytfgqgtkveik
rtvaapsvfifppsdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqd
skdstyslsstltlskadyekhkvyacevthqglsspvtksfnrgec

    Sequence, based on observed residues (ATOM records):
    >7nddL (L:)
iqltqspgtlslspgeratlscrasqsisgnylawyqhkpgqaprlliygastratgipd
rfsgsgsgtdftltisrlepedfavyycqqygssytfgqgtkveik