PDB entry 7dk2

View 7dk2 on RCSB PDB site
Description: Crystal structure of SARS-CoV-2 Spike RBD in complex with MW07 Fab
Class: immune system/viral protein
Keywords: SARS-CoV-2, Spike, RBD, Antibody, ADE, VIRUS, IMMUNE SYSTEM-VIRAL PROTEIN complex
Deposited on 2020-11-22, released 2021-12-08
The last revision prior to the SCOPe 2.08 freeze date was dated 2021-12-08, with a file datestamp of 2021-12-03.
Experiment type: XRAY
Resolution: 3 Å
R-factor: N/A
AEROSPACI score: 0.2 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: MW07 heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7DK2 (0-222)
    Domains in SCOPe 2.08: d7dk2a_
  • Chain 'B':
    Compound: MW07 light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7DK2 (0-213)
    Domains in SCOPe 2.08: d7dk2b_
  • 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): Domains in SCOPe 2.08: d7dk2c_
  • Chain 'D':
    Compound: MW07 heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7DK2 (0-222)
    Domains in SCOPe 2.08: d7dk2d_
  • Chain 'E':
    Compound: MW07 light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7DK2 (0-213)
    Domains in SCOPe 2.08: d7dk2e_
  • Chain 'F':
    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: d7dk2f_
  • Chain 'G':
    Compound: MW07 heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7DK2 (0-222)
    Domains in SCOPe 2.08: d7dk2g_
  • Chain 'H':
    Compound: MW07 light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7DK2 (0-213)
    Domains in SCOPe 2.08: d7dk2h_
  • Chain 'I':
    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: d7dk2i_
  • Chain 'J':
    Compound: MW07 heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7DK2 (0-222)
    Domains in SCOPe 2.08: d7dk2j_
  • Chain 'K':
    Compound: MW07 light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7DK2 (0-213)
    Domains in SCOPe 2.08: d7dk2k_
  • Chain 'L':
    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: d7dk2l_
  • Heterogens: NAG, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >7dk2A (A:)
evqlvesggglvqpggslrlscaasgftfssywmswvrqapgkglewvanikqdasekyy
ldslkgrftisrdnaknslylqmnslraedtavyycardlgilwfgdypwgqgtlvtvss
astkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqss
glyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepksc

  • Chain 'B':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >7dk2B (B:)
diqmtqspsslsasvgdrvtitcrasqgisnslawyqqkpgkapklllyaastlesgvps
rfsgsgsgtdftltisslqpedfatyycqqfystprtfgqgtkveikrtvaapsvfifpp
sdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstlt
lskadyekhkvyacevthqglsspvtksfnrgec

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >7dk2C (C:)
rvqptesivrfpnitnlcpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfk
cygvsptklndlcftnvyadsfvirgdevrqiapgqtgkiadynyklpddftgcviawns
nnldskvggnynylyrlfrksnlkpferdisteiyqagstpcngvegfncyfplqsygfq
ptngvgyqpyrvvvlsfellhapatvcgpkkstnlvknkcvnf

    Sequence, based on observed residues (ATOM records): (download) 
    >7dk2C (C:)
cpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygvsptklndlcftnv
yadsfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnldskvggnynylyrl
frksnlkpferdisteiyqagstpcngvegfncyfplqsygfqptngvgyqpyrvvvlsf
ellhapatvcg

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >7dk2D (D:)
evqlvesggglvqpggslrlscaasgftfssywmswvrqapgkglewvanikqdasekyy
ldslkgrftisrdnaknslylqmnslraedtavyycardlgilwfgdypwgqgtlvtvss
astkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqss
glyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepksc

    Sequence, based on observed residues (ATOM records): (download) 
    >7dk2D (D:)
evqlvesggglvqpggslrlscaasgftfssywmswvrqapgkglewvanikqdasekyy
ldslkgrftisrdnaknslylqmnslraedtavyycardlgilwfgdypwgqgtlvtvss
astkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqss
glyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepks

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >7dk2E (E:)
diqmtqspsslsasvgdrvtitcrasqgisnslawyqqkpgkapklllyaastlesgvps
rfsgsgsgtdftltisslqpedfatyycqqfystprtfgqgtkveikrtvaapsvfifpp
sdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstlt
lskadyekhkvyacevthqglsspvtksfnrgec

    Sequence, based on observed residues (ATOM records): (download) 
    >7dk2E (E:)
diqmtqspsslsasvgdrvtitcrasqgisnslawyqqkpgkapklllyaastlesgvps
rfsgsgsgtdftltisslqpedfatyycqqfystprtfgqgtkveikrtvaapsvfifpp
sdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstlt
lskadyekhkvyacevthqglsspvtksfnrge

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >7dk2F (F:)
rvqptesivrfpnitnlcpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfk
cygvsptklndlcftnvyadsfvirgdevrqiapgqtgkiadynyklpddftgcviawns
nnldskvggnynylyrlfrksnlkpferdisteiyqagstpcngvegfncyfplqsygfq
ptngvgyqpyrvvvlsfellhapatvcgpkkstnlvknkcvnf

    Sequence, based on observed residues (ATOM records): (download) 
    >7dk2F (F:)
cpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygvsptklndlcftnv
yadsfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnldskvggnynylyrl
frksnlkpferdisteiyqagstpcngvegfncyfplqsygfqptngvgyqpyrvvvlsf
ellhapatvc

  • Chain 'G':
    Sequence, based on SEQRES records: (download) 
    >7dk2G (G:)
evqlvesggglvqpggslrlscaasgftfssywmswvrqapgkglewvanikqdasekyy
ldslkgrftisrdnaknslylqmnslraedtavyycardlgilwfgdypwgqgtlvtvss
astkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqss
glyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepksc

    Sequence, based on observed residues (ATOM records): (download) 
    >7dk2G (G:)
evqlvesggglvqpggslrlscaasgftfssywmswvrqapgkglewvanikqdasekyy
ldslkgrftisrdnaknslylqmnslraedtavyycardlgilwfgdypwgqgtlvtvss
astkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqss
glyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepk

  • Chain 'H':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >7dk2H (H:)
diqmtqspsslsasvgdrvtitcrasqgisnslawyqqkpgkapklllyaastlesgvps
rfsgsgsgtdftltisslqpedfatyycqqfystprtfgqgtkveikrtvaapsvfifpp
sdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstlt
lskadyekhkvyacevthqglsspvtksfnrgec

  • Chain 'I':
    Sequence, based on SEQRES records: (download) 
    >7dk2I (I:)
rvqptesivrfpnitnlcpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfk
cygvsptklndlcftnvyadsfvirgdevrqiapgqtgkiadynyklpddftgcviawns
nnldskvggnynylyrlfrksnlkpferdisteiyqagstpcngvegfncyfplqsygfq
ptngvgyqpyrvvvlsfellhapatvcgpkkstnlvknkcvnf

    Sequence, based on observed residues (ATOM records): (download) 
    >7dk2I (I:)
cpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygvsptklndlcftnv
yadsfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnldskvggnynylyrl
frksnlkpferdisteiyqagstpcngvegfncyfplqsygfqptngvgyqpyrvvvlsf
ellhapatv

  • Chain 'J':
    Sequence, based on SEQRES records: (download) 
    >7dk2J (J:)
evqlvesggglvqpggslrlscaasgftfssywmswvrqapgkglewvanikqdasekyy
ldslkgrftisrdnaknslylqmnslraedtavyycardlgilwfgdypwgqgtlvtvss
astkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqss
glyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepksc

    Sequence, based on observed residues (ATOM records): (download) 
    >7dk2J (J:)
evqlvesggglvqpggslrlscaasgftfssywmswvrqapgkglewvanikqdasekyy
ldslkgrftisrdnaknslylqmnslraedtavyycardlgilwfgdypwgqgtlvtvss
astkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqss
glyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepk

  • Chain 'K':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >7dk2K (K:)
diqmtqspsslsasvgdrvtitcrasqgisnslawyqqkpgkapklllyaastlesgvps
rfsgsgsgtdftltisslqpedfatyycqqfystprtfgqgtkveikrtvaapsvfifpp
sdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstlt
lskadyekhkvyacevthqglsspvtksfnrgec

  • Chain 'L':
    Sequence, based on SEQRES records: (download) 
    >7dk2L (L:)
rvqptesivrfpnitnlcpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfk
cygvsptklndlcftnvyadsfvirgdevrqiapgqtgkiadynyklpddftgcviawns
nnldskvggnynylyrlfrksnlkpferdisteiyqagstpcngvegfncyfplqsygfq
ptngvgyqpyrvvvlsfellhapatvcgpkkstnlvknkcvnf

    Sequence, based on observed residues (ATOM records): (download) 
    >7dk2L (L:)
cpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygvsptklndlcftnv
yadsfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnldskvggnynylyrl
frksnlkpferdisteiyqagstpcngvegfncyfplqsygfqptngvgyqpyrvvvlsf
ellhapatvcg