PDB entry 7bek

View 7bek on RCSB PDB site
Description: Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-158 Fab (crystal form 2)
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 2020-12-23, 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: 2.04 Å
R-factor: N/A
AEROSPACI score: 0.38 (click here for full SPACI score report)

Chains and heterogens:

  • 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
      • engineered mutation (203)
    Domains in SCOPe 2.08: d7beke_
  • Chain 'H':
    Compound: COVOX-158 heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7BEK (0-End)
    Domains in SCOPe 2.08: d7bekh_
  • Chain 'L':
    Compound: COVOX-158 light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7BEK (0-213)
    Domains in SCOPe 2.08: d7bekl1, d7bekl2
  • Heterogens: PEG, GOL, SO4, CL, TRS, HOH

PDB Chain Sequences:

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

    Sequence, based on observed residues (ATOM records): (download) 
    >7bekE (E:)
nlcpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygvsptklndlcft
nvyadsfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnldskvggnynyly
rlfrksnlkpferdisteiyqagstpcngvegfncyfplqsygfqptngvgyqpyrvvvl
sfellhapatvcgk

  • Chain 'H':
    Sequence, based on SEQRES records: (download) 
    >7bekH (H:)
evqllesggdliqpggslrlscaasgvtvssnymswvrqapgkglewvsiiypggstfya
dsvkgrftisrdnskntlylqmhslraedtavyycardlgsgdmdvwgkgttvtvssast
kgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqssgly
slssvvtvpssslgtqtyicnvnhkpsntkvdkkvepkscdk

    Sequence, based on observed residues (ATOM records): (download) 
    >7bekH (H:)
evqllesggdliqpggslrlscaasgvtvssnymswvrqapgkglewvsiiypggstfya
dsvkgrftisrdnskntlylqmhslraedtavyycardlgsgdmdvwgkgttvtvssast
kgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqssgly
slssvvtvpssslgtqtyicnvnhkpsntkvdkkvepksc

  • Chain 'L':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >7bekL (L:)
divmtqspsflsasvgdrvtitcrasqgissylawyqqkpgkapklliqaastlqsgvps
rfsgsgsgteftltisslqpedfatyycqqlnsyrytfgqgtkveikrtvaapsvfifpp
sdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstlt
lskadyekhkvyacevthqglsspvtksfnrgec