PDB entry 5u3d

View 5u3d on RCSB PDB site
Description: structure of meditope enabled trastuzumab i83e variant
Class: immune system
Keywords: immune system
Deposited on 2016-12-01, released 2018-03-14
The last revision prior to the SCOPe 2.08 freeze date was dated 2018-04-18, with a file datestamp of 2018-04-13.
Experiment type: XRAY
Resolution: 1.77 Å
R-factor: N/A
AEROSPACI score: 0.38 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: memab trastuzumab fab light chain i83e
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 5U3D (0-213)
    Domains in SCOPe 2.08: d5u3da1, d5u3da2
  • Chain 'B':
    Compound: memab trastuzumab fab heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 5U3D (0-End)
    Domains in SCOPe 2.08: d5u3db_
  • Chain 'C':
    Compound: immunoglobulin g binding protein a
    Species: Staphylococcus aureus [TaxId:1280]
    Gene: SPA
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q2UW42 (3-53)
      • expression tag (0-2)
    Domains in SCOPe 2.08: d5u3dc1, d5u3dc2
  • Chain 'E':
    Compound: protein l
    Species: Finegoldia magna [TaxId:1260]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q51918 (4-64)
      • expression tag (2-3)
      • engineered mutation (17)
      • engineered mutation (38)
      • engineered mutation (56-58)
    Domains in SCOPe 2.08: d5u3de1, d5u3de2
  • Heterogens: MRY, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence; same for both SEQRES and ATOM records: (download)
    >5u3dA (A:)
    diqmtqspillsasvgdrvtitcrasqdvntavawyqqrtngsprlliysasflysgvps
    rfsgsrsgtdftltisslqpedeadyycqqhyttpptfgagtkveikrtvaapsvfifpp
    sdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstlt
    lskadyekhkvyacevthqglsspvtksfnrgec
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >5u3dB (B:)
    evqlvesggglvqpggslrlscaasgfnikdtyihwvrqspgkglewvariyptngytry
    adsvkgrftisadtskntaylqmnslraedtaiyycsrwggdgfyamdywgqgtlvtvss
    astkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqss
    glyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepksc
    

    Sequence, based on observed residues (ATOM records): (download)
    >5u3dB (B:)
    evqlvesggglvqpggslrlscaasgfnikdtyihwvrqspgkglewvariyptngytry
    adsvkgrftisadtskntaylqmnslraedtaiyycsrwggdgfyamdywgqgtlvtvss
    astkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqss
    glyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepk
    

  • Chain 'C':
    Sequence; same for both SEQRES and ATOM records: (download)
    >5u3dC (C:)
    gsynkdqqsafyeilnmpnlneaqrngfiqslkddpsqstnvlgeakklnesqa
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >5u3dE (E:)
    sgsevtikvnlifadgkiqtaefkgtfeeataeayryaallakvngeytadledggnhmn
    ikfag
    

    Sequence, based on observed residues (ATOM records): (download)
    >5u3dE (E:)
    sevtikvnlifadgkiqtaefkgtfeeataeayryaallakvngeytadledggnhmnik
    fag