PDB entry 6xdg

View 6xdg on RCSB PDB site
Description: complex of sars-cov-2 receptor binding domain with the fab fragments of two neutralizing antibodies
Deposited on 2020-06-10, released 2020-06-24
The last revision was dated 2021-01-27, with a file datestamp of 2021-01-22.
Experiment type: EM
Resolution: 3.9 Å
R-factor: N/A
AEROSPACI score: 0.08 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: REGN10987 antibody Fab fragment light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6XDG
  • Chain 'B':
    Compound: REGN10933 antibody Fab fragment heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6XDG (0-End)
  • Chain 'C':
    Compound: REGN10987 antibody Fab fragment heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6XDG (0-End)
  • Chain 'D':
    Compound: REGN10933 antibody Fab fragment light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6XDG (0-213)
  • Chain 'E':
    Compound: Spike protein S1
    Species: Severe acute respiratory syndrome coronavirus 2 [TaxId:2697049]
    Gene: S, 2
    Database cross-references and differences (RAF-indexed):

PDB Chain Sequences:
This PDB entry is not classified in SCOPe 2.08, so the chain sequences below are not included in the ASTRAL sequence sets.

  • Chain 'A':
    Sequence, based on SEQRES records:
    >6xdgA (A:)
qsaltqpasvsgspgqsitisctgtssdvggynyvswyqqhpgkapklmiydvskrpsgv
snrfsgsksgntasltisglqsedeadyycnsltsistwvfgggtkltvlgqpkaapsvt
lfppsseelqankatlvclisdfypgavtvawkadsspvkagvetttpskqsnnkyaass
ylsltpeqwkshrsyscqvthegstvektvaptecs

    Sequence, based on observed residues (ATOM records):
    >6xdgA (A:)
altqpasvsgspgqsitisctgtssdvggynyvswyqqhpgkapklmiydvskrpsgvsn
rfsgsksgntasltisglqsedeadyycnsltsistwvfgggtkltvlgqpkaapsvtlf
ppsseelqankatlvclisdfypgavtvawkadsspvkagvetttpskqsnnkyaassyl
sltpeqwkshrsyscqvthegstvektvapt

  • Chain 'B':
    Sequence, based on SEQRES records:
    >6xdgB (B:)
qvqlvesggglvkpggslrlscaasgftfsdyymswirqapgkglewvsyitysgstiyy
adsvkgrftisrdnaksslylqmnslraedtavyycardrgttmvpfdywgqgtlvtvss
astkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqss
glyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepkscdkt

    Sequence, based on observed residues (ATOM records):
    >6xdgB (B:)
qvqlvesggglvkpggslrlscaasgftfsdyymswirqapgkglewvsyitysgstiyy
adsvkgrftisrdnaksslylqmnslraedtavyycardrgttmvpfdywgqgtlvtvss
astkgpsvfplaptaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqssglyslssv
vtvpssslgtqtyicnvnhkpsntkvdkkvep

  • Chain 'C':
    Sequence, based on SEQRES records:
    >6xdgC (C:)
qvqlvesgggvvqpgrslrlscaasgftfsnyamywvrqapgkglewvavisydgsnkyy
adsvkgrftisrdnskntlylqmnslrtedtavyycasgsdygdyllvywgqgtlvtvss
astkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqss
glyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepkscdk

    Sequence, based on observed residues (ATOM records):
    >6xdgC (C:)
qvqlvesgggvvqpgrslrlscaasgftfsnyamywvrqapgkglewvavisydgsnkyy
adsvkgrftisrdnskntlylqmnslrtedtavyycasgsdygdyllvywgqgtlvtvss
astkgpsvfplaptaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqssglyslssv
vtvpssslgtqtyicnvnhkpsntkvdkkvep

  • Chain 'D':
    Sequence; same for both SEQRES and ATOM records:
    >6xdgD (D:)
diqmtqspsslsasvgdrvtitcqasqditnylnwyqqkpgkapklliyaasnletgvps
rfsgsgsgtdftftisglqpediatyycqqydnlpltfgggtkveikrtvaapsvfifpp
sdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstlt
lskadyekhkvyacevthqglsspvtksfnrgec

  • Chain 'E':
    Sequence, based on SEQRES records:
    >6xdgE (E:)
rvqptesivrfpnitnlcpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfk
cygvsptklndlcftnvyadsfvirgdevrqiapgqtgkiadynyklpddftgcviawns
nnldskvggnynylyrlfrksnlkpferdisteiyqagstpcngvegfncyfplqsygfq
ptngvgyqpyrvvvlsfellhapatvcgpkkstnlvknkcvnfeqkliseedlggeqkli
seedlhhhhhh

    Sequence, based on observed residues (ATOM records):
    >6xdgE (E:)
tnlcpfgevfnatrfasvyawnrkrisncvadysvlynsasfstfkcygvsptklndlcf
tnvyadsfvirgdevrqiapgqtgkiadynyklpddftgcviawnsnnldskvggnynyl
yrlfrksnlkpferdisteiyqagstpcngvegfncyfplqsygfqptngvgyqpyrvvv
lsfellhapatvcg