PDB entry 7bep

View 7bep on RCSB PDB site
Description: Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in a ternary complex with COVOX-384 and S309 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: 2.61 Å
R-factor: N/A
AEROSPACI score: 0.26 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: COVOX-384 heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7BEP
    Domains in SCOPe 2.08: d7bepa_
  • Chain 'B':
    Compound: COVOX-384 light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7BEP
    Domains in SCOPe 2.08: d7bepb1
  • 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 (9-204)
      • expression tag (8)
      • engineered mutation (203)
    Domains in SCOPe 2.08: d7bepc1, d7bepc2
  • Chain 'D':
    Compound: COVOX-384 heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7BEP
    Domains in SCOPe 2.08: d7bepd_
  • 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 (9-204)
      • expression tag (8)
      • engineered mutation (203)
    Domains in SCOPe 2.08: d7bepe1, d7bepe2
  • Chain 'F':
    Compound: COVOX-384 light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7BEP
    Domains in SCOPe 2.08: d7bepf1
  • Chain 'G':
    Compound: S309 heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7BEP (0-231)
  • Chain 'H':
    Compound: S309 heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7BEP (0-End)
  • Chain 'I':
    Compound: S309 light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7BEP (0-213)
    Domains in SCOPe 2.08: d7bepi1, d7bepi2
  • Chain 'L':
    Compound: S309 light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7BEP (0-213)
    Domains in SCOPe 2.08: d7bepl1, d7bepl2
  • Heterogens: IMD, CL, GLU, GLY, PGE, GOL, PG4, PEG, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >7bepA (A:)
ilflvatatgvhsevqlvesggglvkpgeslrlscaasgftfsdyymtwirqapgkglew
vsyirssghtiyyadsvkgrftisrdnaknslylqmnslrvedtavyycarggvlrflew
plnafdiwgqgtmvtvssastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswn
sgaltsgvhtfpavlqssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepks
cdk

    Sequence, based on observed residues (ATOM records): (download) 
    >7bepA (A:)
evqlvesggglvkpgeslrlscaasgftfsdyymtwirqapgkglewvsyirssghtiyy
adsvkgrftisrdnaknslylqmnslrvedtavyycarggvlrflewplnafdiwgqgtm
vtvssastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpa
vlqssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepksc

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >7bepB (B:)
ilflvatatgvhsdiqltqspsslsasvgdrvtitcrasqgisnylawyqqkpgkvpkll
iyaastlqsgvpsrfsgsgsgtdftltisslqpedvatyycqkynnalgtfgqgtkveik
rtvaapsvfifppsdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqd
skdstyslsstltlskadyekhkvyacevthqglsspvtksfnrgec

    Sequence, based on observed residues (ATOM records): (download) 
    >7bepB (B:)
lflvadiqltqspsslsasvgdrvtitcrasqgisnylawyqqkpgkvpklliyaastlq
sgvpsrfsgsgsgtdftltisslqpedvatyycqkynnalgtfgqgtkveikrtvaapsv
fifppsdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstysl
sstltlskadyekhkvyacevthqglsspvtksfnrge

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

    Sequence, based on observed residues (ATOM records): (download) 
    >7bepC (C:)
htnlcpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygvsptklndlc
ftnvyadsfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnldskvggnyny
lyrlfrksnlkpferdisteiyqagstpcngvegfncyfplqsygfqptngvgyqpyrvv
vlsfellhapatvcgkk

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >7bepD (D:)
ilflvatatgvhsevqlvesggglvkpgeslrlscaasgftfsdyymtwirqapgkglew
vsyirssghtiyyadsvkgrftisrdnaknslylqmnslrvedtavyycarggvlrflew
plnafdiwgqgtmvtvssastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswn
sgaltsgvhtfpavlqssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepks
cdk

    Sequence, based on observed residues (ATOM records): (download) 
    >7bepD (D:)
evqlvesggglvkpgeslrlscaasgftfsdyymtwirqapgkglewvsyirssghtiyy
adsvkgrftisrdnaknslylqmnslrvedtavyycarggvlrflewplnafdiwgqgtm
vtvssastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpa
vlqssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepks

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

    Sequence, based on observed residues (ATOM records): (download) 
    >7bepE (E:)
htnlcpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygvsptklndlc
ftnvyadsfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnldskvggnyny
lyrlfrksnlkpferdisteiyqagstpcngvegfncyfplqsygfqptngvgyqpyrvv
vlsfellhapatvcgkk

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >7bepF (F:)
ilflvatatgvhsdiqltqspsslsasvgdrvtitcrasqgisnylawyqqkpgkvpkll
iyaastlqsgvpsrfsgsgsgtdftltisslqpedvatyycqkynnalgtfgqgtkveik
rtvaapsvfifppsdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqd
skdstyslsstltlskadyekhkvyacevthqglsspvtksfnrgec

    Sequence, based on observed residues (ATOM records): (download) 
    >7bepF (F:)
lflvadiqltqspsslsasvgdrvtitcrasqgisnylawyqqkpgkvpklliyaastlq
sgvpsrfsgsgsgtdftltisslqpedvatyycqkynnalgtfgqgtkveikrtvaapsv
fifppsdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstysl
sstltlskadyekhkvyacevthqglsspvtksfnrge

  • Chain 'G':
    No sequence available.

  • Chain 'H':
    No sequence available.

  • Chain 'I':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >7bepI (I:)
eivltqspgtlslspgeratlscrasqtvsstslawyqqkpgqaprlliygassratgip
drfsgsgsgtdftltisrlepedfavyycqqhdtsltfgggtkveikrtvaapsvfifpp
sdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstlt
lskadyekhkvyacevthqglsspvtksfnrgec

  • Chain 'L':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >7bepL (L:)
eivltqspgtlslspgeratlscrasqtvsstslawyqqkpgqaprlliygassratgip
drfsgsgsgtdftltisrlepedfavyycqqhdtsltfgggtkveikrtvaapsvfifpp
sdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstlt
lskadyekhkvyacevthqglsspvtksfnrgec