PDB entry 6zcz

View 6zcz on RCSB PDB site
Description: Crystal structure of receptor binding domain of SARS-CoV-2 Spike glycoprotein in ternary complex with EY6A Fab and a nanobody.
Class: viral protein
Keywords: EY6a, RBD, Spike glycoprotein, SARS-CoV-2, human neutralizing antibody, VIRAL PROTEIN, IMMUNE SYSTEM
Deposited on 2020-06-12, released 2020-06-24
The last revision prior to the SCOPe 2.08 freeze date was dated 2021-02-10, with a file datestamp of 2021-02-05.
Experiment type: XRAY
Resolution: 2.65 Å
R-factor: N/A
AEROSPACI score: 0.25 (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 (9-End)
      • engineered mutation (203)
    Domains in SCOPe 2.08: d6zcze_
  • Chain 'F':
    Compound: Nanobody
    Species: LAMA GLAMA [TaxId:9844]
    Database cross-references and differences (RAF-indexed):
    • PDB 6ZCZ
    Domains in SCOPe 2.08: d6zczf_
  • Chain 'H':
    Compound: EY6A heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6ZCZ (0-End)
    Domains in SCOPe 2.08: d6zczh_
  • Chain 'L':
    Compound: EY6A light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6ZCZ (0-214)
    Domains in SCOPe 2.08: d6zczl1, d6zczl2
  • Heterogens: NAG, CL, MG

PDB Chain Sequences:

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >6zczE (E:)
etghhhhhhtnlcpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygvs
ptklndlcftnvyadsfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnlds
kvggnynylyrlfrksnlkpferdisteiyqagstpcngvegfncyfplqsygfqptngv
gyqpyrvvvlsfellhapatvcgkk

    Sequence, based on observed residues (ATOM records): (download) 
    >6zczE (E:)
tnlcpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygvsptklndlcf
tnvyadsfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnldskvggnynyl
yrlfrksnlkpferdisteiyqagstpcngvegfncyfplqsygfqptngvgyqpyrvvv
lsfellhapatvcgk

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >6zczF (F:)
qvqlvesggglmqaggslrlscavsgrtfstaamgwfrqapgkerefvaairwsggsayy
adsvkgrftisrdkakntvylqmnslkyedtavyycaqthyvsyllsdyatwpydywgqg
tqvtvssgpggqhhhhhhgaeqkliseedls

    Sequence, based on observed residues (ATOM records): (download) 
    >6zczF (F:)
vqlvesggglmqaggslrlscavsgrtfstaamgwfrqapgkerefvaairwsggsayya
dsvkgrftisrdkakntvylqmnslkyedtavyycaqthyvsyllsdyatwpydywgqgt
qvtvs

  • Chain 'H':
    Sequence, based on SEQRES records: (download) 
    >6zczH (H:)
evqlvesgggvvqpgrslrlscaasaftfssydmhwvrqapgkglewvavisydgsnkyy
adsvkgrftisrdnskntlylqmnslraedtavyycakdggklwvyyfdywgqgtlvtvs
sastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqs
sglyslssvvtvpssslgtqtyicnvnhkpsntkvdkrvepkscdk

    Sequence, based on observed residues (ATOM records): (download) 
    >6zczH (H:)
evqlvesgggvvqpgrslrlscaasaftfssydmhwvrqapgkglewvavisydgsnkyy
adsvkgrftisrdnskntlylqmnslraedtavyycakdggklwvyyfdywgqgtlvtvs
sastkgpsvfplapssgtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqssglys
lssvvtvpssslgtqtyicnvnhkpsntkvdkrvepksc

  • Chain 'L':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >6zczL (L:)
diqmtqspsslsasvgdrvtitcrasqsissylnwyqqkpgkapklliyaasslqsgvps
rfsgsgsgtdftltisslqpedfatyycqqsystlaltfgggtkveikrtvaapsvfifp
psdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstl
tlskadyekhkvyacevthqglsspvtksfnrgec