PDB entry 7kn6

View 7kn6 on RCSB PDB site
Description: Crystal structure of SARS-CoV-2 receptor binding domain complexed with nanobody VHH V and antibody Fab CC12.3
Class: viral protein/immune system
Keywords: SARS-CoV-2, Nanobody, Spike, Coronavirus, COVID-19, IMMUNE SYSTEM, Nanobody-antigen complex, single-domain antibody, Antibody, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex
Deposited on 2020-11-04, released 2021-01-20
The last revision prior to the SCOPe 2.08 freeze date was dated 2021-02-24, with a file datestamp of 2021-02-19.
Experiment type: XRAY
Resolution: 2.55 Å
R-factor: N/A
AEROSPACI score: 0.26 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Spike protein S1
    Species: Severe acute respiratory syndrome coronavirus 2 [TaxId:2697049]
    Gene: S, 2
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d7kn6a_
  • Chain 'C':
    Compound: vhh v
    Species: Vicugna pacos [TaxId:30538]
    Database cross-references and differences (RAF-indexed):
    • PDB 7KN6 (0-End)
    Domains in SCOPe 2.08: d7kn6c_
  • Chain 'H':
    Compound: CC12.3 Fab heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7KN6 (0-End)
    Domains in SCOPe 2.08: d7kn6h_
  • Chain 'L':
    Compound: CC12.3 Fab light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7KN6 (0-End)
    Domains in SCOPe 2.08: d7kn6l1, d7kn6l2
  • Heterogens: NAG

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >7kn6A (A:)
rvqptesivrfpnitnlcpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfk
cygvsptklndlcftnvyadsfvirgdevrqiapgqtgkiadynyklpddftgcviawns
nnldskvggnynylyrlfrksnlkpferdisteiyqagstpcngvegfncyfplqsygfq
ptngvgyqpyrvvvlsfellhapatvcgpkkstnlvknkcvnfsghhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >7kn6A (A:)
nlcpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygvsptklndlcft
nvyadsfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnldskvggnynyly
rlfrksnlkpferdisteiyqagstpcngvegfncyfplqsygfqptngvgyqpyrvvvl
sfeatvc

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >7kn6C (C:)
qvqlvetggglvqpggslrlscaasgftfssyamgwarqvpgkglewvsyiysdgsteyq
dsvkgrftisrdnakstvylqmnslkpedtavyycategslggwgrdfgswgqgtqvtvs
sgglpetgghhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >7kn6C (C:)
qvqlvetggglvqpggslrlscaasgftfssyamgwarqvpgkglewvsyiysdgsteyq
dsvkgrftisrdnakstvylqmnslkpedtavyycategslggwgrdfgswgqgtqvtvs
s

  • Chain 'H':
    Sequence, based on SEQRES records: (download) 
    >7kn6H (H:)
qvqlvesgggliqpggslrlscaasgftvssnymswvrqapgkglewvsviysggstfya
dsvkgrftisrdnskstlylqmnslrvedtavyycardfgdfyfdywgqgtlvtvssast
kgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqssgly
slssvvtvpssslgtqtyicnvnhkpsntkvdkkvepksc

    Sequence, based on observed residues (ATOM records): (download) 
    >7kn6H (H:)
qvqlvesgggliqpggslrlscaasgftvssnymswvrqapgkglewvsviysggstfya
dsvkgrftisrdnskstlylqmnslrvedtavyycardfgdfyfdywgqgtlvtvssast
kgpsvfplapsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqssglyslssv
vtvpssslgtqtyicnvnhkpsntkvdkkvep

  • Chain 'L':
    Sequence, based on SEQRES records: (download) 
    >7kn6L (L:)
eivltqspgtlslspgeratlscrasqsvssylawyqqkpgqaprlliygassratgipd
rfsgsgsgtdftltisrlepedfavyycqqygssprtfgqgtkleikrtvaapsvfifpp
sdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstlt
lskadyekhkvyacevthqglsspvtksfnrgec

    Sequence, based on observed residues (ATOM records): (download) 
    >7kn6L (L:)
eivltqspgtlslspgeratlscrasqsvssylawyqqkpgqaprlliygassratgipd
rfsgsgsgtdftltisrlepedfavyycqqygssprtfgqgtkleikrtvaapsvfifpp
sdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstlt
lskadyekhkvyacevthqglsspvtksfnrge