PDB entry 7ben

View 7ben on RCSB PDB site
Description: Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in a ternary complex with COVOX-253 and COVOX-75 Fabs
Class: viral protein/immune system
Keywords: SARS-CoV-2, antibody, germline, V-gene, receptor-binding-domain, spike, neutralisation, protection, glycosylation, valency, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN, IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex
Deposited on 2020-12-24, released 2021-03-03
The last revision prior to the SCOPe 2.08 freeze date was dated 2021-04-28, with a file datestamp of 2021-04-23.
Experiment type: XRAY
Resolution: 2.5 Å
R-factor: N/A
AEROSPACI score: 0.29 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: COVOX-75 heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7BEN (0-End)
    Domains in SCOPe 2.08: d7bena_
  • Chain 'B':
    Compound: COVOX-75 light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7BEN (0-End)
    Domains in SCOPe 2.08: d7benb1, d7benb2
  • Chain 'C':
    Compound: Spike glycoprotein
    Species: Severe acute respiratory syndrome coronavirus 2 [TaxId:2697049]
    Gene: S, 2
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d7benc_
  • Chain 'D':
    Compound: COVOX-253 heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7BEN (0-End)
    Domains in SCOPe 2.08: d7bend_
  • Chain 'E':
    Compound: Spike glycoprotein
    Species: Severe acute respiratory syndrome coronavirus 2 [TaxId:2697049]
    Gene: S, 2
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d7bene_
  • Chain 'F':
    Compound: COVOX-253 light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7BEN (0-End)
    Domains in SCOPe 2.08: d7benf1, d7benf2
  • Chain 'G':
    Compound: COVOX-75 heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7BEN (0-End)
    Domains in SCOPe 2.08: d7beng_
  • Chain 'H':
    Compound: COVOX-253 heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7BEN (0-End)
    Domains in SCOPe 2.08: d7benh_
  • Chain 'I':
    Compound: COVOX-75 light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7BEN (0-End)
    Domains in SCOPe 2.08: d7beni1, d7beni2
  • Chain 'L':
    Compound: COVOX-253 light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7BEN (0-End)
    Domains in SCOPe 2.08: d7benl1, d7benl2
  • Heterogens: FUC, NAG, IMD, GOL, BR, PG6, PEG, IOD, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >7benA (A:)
qvqlvesgggvvqpgrslrlscaasgftfnnyplhwvrqapgkgpewvavisqdggnkyy
vdsvkgrftisrdnskntlylqmnnlraedtalyycardvvvvvaarnhyyngmdvwgqg
ttvtvssastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtf
pavlqssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepkscdk

    Sequence, based on observed residues (ATOM records): (download) 
    >7benA (A:)
qvqlvesgggvvqpgrslrlscaasgftfnnyplhwvrqapgkgpewvavisqdggnkyy
vdsvkgrftisrdnskntlylqmnnlraedtalyycardvvvvvaarnhyyngmdvwgqg
ttvtvssastkgpsvfplapsskstaalgclvkdyfpepvtvswnsgaltsgvhtfpavl
qssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepk

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >7benB (B:)
diqltqspssvsasvgdrvtitcrasqgisswlawyqqkpgkapklliyavsslqsgvps
rfsgsgsgtdftltisslqpedfatyycqqaksfpftfgpgtkveikrtvaapsvfifpp
sdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstlt
lskadyekhkvyacevthqglsspvtksfnrgec

    Sequence, based on observed residues (ATOM records): (download) 
    >7benB (B:)
diqltqspssvsasvgdrvtitcrasqgisswlawyqqkpgkapklliyavsslqsgvps
rfsgsgsgtdftltisslqpedfatyycqqaksfpftfgpgtkveikrtvaapsvfifpp
sdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstlt
lskadyekhkvyacevthqglsspvtksfnrge

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >7benC (C:)
etghhhhhhtnlcpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygvs
ptklndlcftnvyadsfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnlds
kvggnynylyrlfrksnlkpferdisteiyqagstpcngvegfncyfplqsygfqptngv
gyqpyrvvvlsfellhapatvcgkk

    Sequence, based on observed residues (ATOM records): (download) 
    >7benC (C:)
cpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygvsptklcftnvyad
sfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnldskvggnynylyrlfrk
snlkpferdisteiyqagstpcngvegfncyfplqsygfqptngvgyqpyrvvvlsfe

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >7benD (D:)
qvqlvqsgpevkkpgtsvkvsckasgftfttsavqwvrqargqrlewigwivvgsgntny
aqkfqervtitrdmstttaymelsslrsedtavyfcaaphcnstscydafdiwgqgtmvt
vssastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavl
qssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepkscdk

    Sequence, based on observed residues (ATOM records): (download) 
    >7benD (D:)
qvqlvqsgpevkkpgtsvkvsckasgftfttsavqwvrqargqrlewigwivvgsgntny
aqkfqervtitrdmstttaymelsslrsedtavyfcaaphcnstscydafdiwgqgtmvt
vssastkgpsvfplapssgtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqssgl
yslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepk

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >7benE (E:)
etghhhhhhtnlcpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygvs
ptklndlcftnvyadsfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnlds
kvggnynylyrlfrksnlkpferdisteiyqagstpcngvegfncyfplqsygfqptngv
gyqpyrvvvlsfellhapatvcgkk

    Sequence, based on observed residues (ATOM records): (download) 
    >7benE (E:)
pfgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygvspndlcftnvyads
fvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnldskvggnynylyrlfrks
nlkpferdisteiyqagstpcngvegfncyfplqsygfqptngvgyqpyrvvvlsfe

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >7benF (F:)
diqmtqspgtlslspgegatlscrasqsvsssylawyqqkpgqaprlliygassgatgip
drfsgsgsgtdftltisrlepedfavyycqqygsspytfgqgtkveikrtvaapsvfifp
psdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstl
tlskadyekhkvyacevthqglsspvtksfnrgec

    Sequence, based on observed residues (ATOM records): (download) 
    >7benF (F:)
diqmtqspgtlslspgegatlscrasqsvsssylawyqqkpgqaprlliygassgatgip
drfsgsgsgtdftltisrlepedfavyycqqygsspytfgqgtkveikrtvaapsvfifp
psdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstl
tlskadyekhkvyacevthqglsspvtksfnrge

  • Chain 'G':
    Sequence, based on SEQRES records: (download) 
    >7benG (G:)
qvqlvesgggvvqpgrslrlscaasgftfnnyplhwvrqapgkgpewvavisqdggnkyy
vdsvkgrftisrdnskntlylqmnnlraedtalyycardvvvvvaarnhyyngmdvwgqg
ttvtvssastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtf
pavlqssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepkscdk

    Sequence, based on observed residues (ATOM records): (download) 
    >7benG (G:)
qvqlvesgggvvqpgrslrlscaasgftfnnyplhwvrqapgkgpewvavisqdggnkyy
vdsvkgrftisrdnskntlylqmnnlraedtalyycardvvvvvaarnhyyngmdvwgqg
ttvtvssastkgpsvfplapsskstaalgclvkdyfpepvtvswnsgaltsgvhtfpavl
qssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepk

  • Chain 'H':
    Sequence, based on SEQRES records: (download) 
    >7benH (H:)
qvqlvqsgpevkkpgtsvkvsckasgftfttsavqwvrqargqrlewigwivvgsgntny
aqkfqervtitrdmstttaymelsslrsedtavyfcaaphcnstscydafdiwgqgtmvt
vssastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavl
qssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepkscdk

    Sequence, based on observed residues (ATOM records): (download) 
    >7benH (H:)
qvqlvqsgpevkkpgtsvkvsckasgftfttsavqwvrqargqrlewigwivvgsgntny
aqkfqervtitrdmstttaymelsslrsedtavyfcaaphcnstscydafdiwgqgtmvt
vssastkgpsvfplapssgtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqssgl
yslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepk

  • Chain 'I':
    Sequence, based on SEQRES records: (download) 
    >7benI (I:)
diqltqspssvsasvgdrvtitcrasqgisswlawyqqkpgkapklliyavsslqsgvps
rfsgsgsgtdftltisslqpedfatyycqqaksfpftfgpgtkveikrtvaapsvfifpp
sdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstlt
lskadyekhkvyacevthqglsspvtksfnrgec

    Sequence, based on observed residues (ATOM records): (download) 
    >7benI (I:)
diqltqspssvsasvgdrvtitcrasqgisswlawyqqkpgkapklliyavsslqsgvps
rfsgsgsgtdftltisslqpedfatyycqqaksfpftfgpgtkveikrtvaapsvfifpp
sdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstlt
lskadyekhkvyacevthqglsspvtksfnrge

  • Chain 'L':
    Sequence, based on SEQRES records: (download) 
    >7benL (L:)
diqmtqspgtlslspgegatlscrasqsvsssylawyqqkpgqaprlliygassgatgip
drfsgsgsgtdftltisrlepedfavyycqqygsspytfgqgtkveikrtvaapsvfifp
psdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstl
tlskadyekhkvyacevthqglsspvtksfnrgec

    Sequence, based on observed residues (ATOM records): (download) 
    >7benL (L:)
diqmtqspgtlslspgegatlscrasqsvsssylawyqqkpgqaprlliygassgatgip
drfsgsgsgtdftltisrlepedfavyycqqygsspytfgqgtkveikrtvaapsvfifp
psdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstl
tlskadyekhkvyacevthqglsspvtksfnrge