PDB entry 7ora

View 7ora on RCSB PDB site
Description: Crystal structure of the T478K mutant receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-45 and COVOX-253 Fabs
Class: viral protein
Keywords: SARS-CoV-2 B.1.1.7 variant, B.1.351 variant, P.1 variant, B.1.617 variant, antibody, receptor-binding-domain, spike, neutralisation, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN
Deposited on 2021-06-04, released 2021-07-07
The last revision prior to the SCOPe 2.08 freeze date was dated 2021-07-21, with a file datestamp of 2021-07-16.
Experiment type: XRAY
Resolution: 2.6 Å
R-factor: N/A
AEROSPACI score: 0.28 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: COVOX-45 Fab heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7ORA (0-225)
    Domains in SCOPe 2.08: d7oraa_
  • Chain 'B':
    Compound: COVOX-45 Fab light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7ORA (0-213)
    Domains in SCOPe 2.08: d7orab_
  • Chain 'C':
    Compound: Spike protein S1
    Species: Severe acute respiratory syndrome coronavirus 2 [TaxId:2697049]
    Gene: S, 2
    Database cross-references and differences (RAF-indexed):
    • Uniprot P0DTC2 (9-204)
      • expression tag (0-8)
      • engineered mutation (154)
      • conflict (203)
    Domains in SCOPe 2.08: d7orac1, d7orac2
  • Chain 'D':
    Compound: COVOX-45 Fab heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7ORA (0-225)
    Domains in SCOPe 2.08: d7orad_
  • Chain 'E':
    Compound: COVOX-45 Fab light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7ORA (0-213)
    Domains in SCOPe 2.08: d7orae_
  • Chain 'F':
    Compound: COVOX-253 Fab heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7ORA (0-227)
    Domains in SCOPe 2.08: d7oraf_
  • Chain 'G':
    Compound: COVOX-253 Fab light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7ORA (0-214)
    Domains in SCOPe 2.08: d7orag_
  • Chain 'H':
    Compound: COVOX-253 Fab heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7ORA (0-227)
    Domains in SCOPe 2.08: d7orah_
  • Chain 'L':
    Compound: COVOX-253 Fab light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7ORA (0-214)
    Domains in SCOPe 2.08: d7oral_
  • Chain 'R':
    Compound: Spike protein S1
    Species: Severe acute respiratory syndrome coronavirus 2 [TaxId:2697049]
    Gene: S, 2
    Database cross-references and differences (RAF-indexed):
    • Uniprot P0DTC2 (9-204)
      • expression tag (0-8)
      • engineered mutation (154)
      • conflict (203)
    Domains in SCOPe 2.08: d7orar1, d7orar2
  • Heterogens: GOL, CL, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >7oraA (A:)
qvqlvesgggvvqpgrslrlscaasgftfstyamhwvrqapgkglewvavlsydgsnkyy
adsvkgrftisrdnskntlylqmnslraedtavyycakggsyayyyymdvwgkgttvtvs
sastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqs
sglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepkscdk

    Sequence, based on observed residues (ATOM records): (download) 
    >7oraA (A:)
qvqlvesgggvvqpgrslrlscaasgftfstyamhwvrqapgkglewvavlsydgsnkyy
adsvkgrftisrdnskntlylqmnslraedtavyycakggsyayyyymdvwgkgttvtvs
sastkgpsvfplapggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqssglysl
ssvvtvpssslgtqtyicnvnhkpsntkvdkkvepk

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >7oraB (B:)
diqltqspsslsasvgdrvtitcqasqdisnylnwyqqkpgkapklliydasnletgvps
rfsgggsgtdftftitslqpediatyycqqydnlpltfgggtkvdikrtvaapsvfifpp
sdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstlt
lskadyekhkvyacevthqglsspvtksfnrgec

    Sequence, based on observed residues (ATOM records): (download) 
    >7oraB (B:)
diqltqspsslsasvgdrvtitcqasqdisnylnwyqqkpgkapklliydasnletgvps
rfsgggsgtdftftitslqpediatyycqqydnlpltfgggtkvdikrtvaapsvfifpp
sdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstlt
lskadyekhkvyacevthqglsspvtksfnr

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

    Sequence, based on observed residues (ATOM records): (download) 
    >7oraC (C:)
hhtnlcpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygvsptklndl
cftnvyadsfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnldskvggnyn
ylyrlfrksnlkpferdisteiyqagskpcngvegfncyfplqsygfqptngvgyqpyrv
vvlsfellhapatvcgk

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >7oraD (D:)
qvqlvesgggvvqpgrslrlscaasgftfstyamhwvrqapgkglewvavlsydgsnkyy
adsvkgrftisrdnskntlylqmnslraedtavyycakggsyayyyymdvwgkgttvtvs
sastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqs
sglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepkscdk

    Sequence, based on observed residues (ATOM records): (download) 
    >7oraD (D:)
qvqlvesgggvvqpgrslrlscaasgftfstyamhwvrqapgkglewvavlsydgsnkyy
adsvkgrftisrdnskntlylqmnslraedtavyycakggsyayyyymdvwgkgttvtvs
sastkgpsvfplapggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqssglysl
ssvvtvpssslgtqtyicnvnhkpsntkvdkkvepk

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >7oraE (E:)
diqltqspsslsasvgdrvtitcqasqdisnylnwyqqkpgkapklliydasnletgvps
rfsgggsgtdftftitslqpediatyycqqydnlpltfgggtkvdikrtvaapsvfifpp
sdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstlt
lskadyekhkvyacevthqglsspvtksfnrgec

    Sequence, based on observed residues (ATOM records): (download) 
    >7oraE (E:)
diqltqspsslsasvgdrvtitcqasqdisnylnwyqqkpgkapklliydasnletgvps
rfsgggsgtdftftitslqpediatyycqqydnlpltfgggtkvdikrtvaapsvfifpp
sdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstlt
lskadyekhkvyacevthqglsspvtksfnr

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

    Sequence, based on observed residues (ATOM records): (download) 
    >7oraF (F:)
qvqlvqsgpevkkpgtsvkvsckasgftfttsavqwvrqargqrlewigwivvgsgntny
aqkfqervtitrdmstttaymelsslrsedtavyfcaaphcnstscydafdiwgqgtmvt
vssastkgpsvfplapsskstgtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqs
sglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepksc

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

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

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

    Sequence, based on observed residues (ATOM records): (download) 
    >7oraH (H:)
qvqlvqsgpevkkpgtsvkvsckasgftfttsavqwvrqargqrlewigwivvgsgntny
aqkfqervtitrdmstttaymelsslrsedtavyfcaaphcnstscydafdiwgqgtmvt
vssastkgpsvfplapsskstgtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqs
sglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepksc

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

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

  • Chain 'R':
    Sequence, based on SEQRES records: (download) 
    >7oraR (R:)
etghhhhhhtnlcpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygvs
ptklndlcftnvyadsfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnlds
kvggnynylyrlfrksnlkpferdisteiyqagskpcngvegfncyfplqsygfqptngv
gyqpyrvvvlsfellhapatvcgkk

    Sequence, based on observed residues (ATOM records): (download) 
    >7oraR (R:)
hhtnlcpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygvsptklndl
cftnvyadsfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnldskvggnyn
ylyrlfrksnlkpferdisteiyqagskpcngvegfncyfplqsygfqptngvgyqpyrv
vvlsfellhapatvcgk