PDB entry 5yoy

View 5yoy on RCSB PDB site
Description: Crystal structure of the human tumor necrosis factor in complex with golimumab Fv
Class: immune system
Keywords: Cytokine, Antibody, IMMUNE SYSTEM
Deposited on 2017-10-31, released 2018-05-09
The last revision prior to the SCOPe 2.07 freeze date was dated 2018-05-09, with a file datestamp of 2018-05-04.
Experiment type: XRAY
Resolution: 2.73 Å
R-factor: N/A
AEROSPACI score: 0.17 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Tumor necrosis factor
    Species: Homo sapiens [TaxId:9606]
    Gene: TNF, TNFA, TNFSF2
    Database cross-references and differences (RAF-indexed):
    • Uniprot P01375 (Start-164)
      • cloning artifact (165-166)
    Domains in SCOPe 2.07: d5yoya1, d5yoya2
  • Chain 'B':
    Compound: Tumor necrosis factor
    Species: Homo sapiens [TaxId:9606]
    Gene: TNF, TNFA, TNFSF2
    Database cross-references and differences (RAF-indexed):
    • Uniprot P01375 (Start-164)
      • cloning artifact (165-166)
    Domains in SCOPe 2.07: d5yoyb1, d5yoyb2
  • Chain 'C':
    Compound: Tumor necrosis factor
    Species: Homo sapiens [TaxId:9606]
    Gene: TNF, TNFA, TNFSF2
    Database cross-references and differences (RAF-indexed):
    • Uniprot P01375 (Start-164)
      • cloning artifact (165-166)
    Domains in SCOPe 2.07: d5yoyc1, d5yoyc2
  • Chain 'D':
    Compound: Golimumab light chain variable region
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 5YOY
    Domains in SCOPe 2.07: d5yoyd_
  • Chain 'E':
    Compound: Golimumab light chain variable region
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 5YOY
    Domains in SCOPe 2.07: d5yoye_
  • Chain 'F':
    Compound: Golimumab light chain variable region
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 5YOY
    Domains in SCOPe 2.07: d5yoyf_
  • Chain 'G':
    Compound: Golimumab heavy chain variable region
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 5YOY (Start-128)
    Domains in SCOPe 2.07: d5yoyg_
  • Chain 'H':
    Compound: Golimumab heavy chain variable region
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 5YOY (Start-128)
    Domains in SCOPe 2.07: d5yoyh_
  • Chain 'I':
    Compound: Golimumab heavy chain variable region
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 5YOY
    Domains in SCOPe 2.07: d5yoyi_
  • Chain 'J':
    Compound: Tumor necrosis factor
    Species: Homo sapiens [TaxId:9606]
    Gene: TNF, TNFA, TNFSF2
    Database cross-references and differences (RAF-indexed):
    • Uniprot P01375 (Start-164)
      • cloning artifact (165)
    Domains in SCOPe 2.07: d5yoyj1, d5yoyj2
  • Chain 'K':
    Compound: Tumor necrosis factor
    Species: Homo sapiens [TaxId:9606]
    Gene: TNF, TNFA, TNFSF2
    Database cross-references and differences (RAF-indexed):
    • Uniprot P01375 (Start-164)
      • cloning artifact (165)
    Domains in SCOPe 2.07: d5yoyk1, d5yoyk2
  • Chain 'L':
    Compound: Tumor necrosis factor
    Species: Homo sapiens [TaxId:9606]
    Gene: TNF, TNFA, TNFSF2
    Database cross-references and differences (RAF-indexed):
    • Uniprot P01375 (Start-164)
      • cloning artifact (165)
    Domains in SCOPe 2.07: d5yoyl1, d5yoyl2
  • Chain 'M':
    Compound: Golimumab light chain variable region
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 5YOY
    Domains in SCOPe 2.07: d5yoym_
  • Chain 'N':
    Compound: Golimumab light chain variable region
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 5YOY
    Domains in SCOPe 2.07: d5yoyn_
  • Chain 'O':
    Compound: Golimumab light chain variable region
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 5YOY
    Domains in SCOPe 2.07: d5yoyo_
  • Chain 'P':
    Compound: Golimumab heavy chain variable region
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 5YOY (Start-128)
    Domains in SCOPe 2.07: d5yoyp_
  • Chain 'Q':
    Compound: Golimumab heavy chain variable region
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 5YOY (Start-128)
    Domains in SCOPe 2.07: d5yoyq_
  • Chain 'R':
    Compound: Golimumab heavy chain variable region
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 5YOY (Start-128)
    Domains in SCOPe 2.07: d5yoyr_
  • Heterogens: HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >5yoyA (A:)
    dykddddkvrsssrtpsdkpvahvvanpqaegqlqwlnrranallangvelrdnqlvvps
    eglyliysqvlfkgqgcpsthvllthtisriavsyqtkvnllsaikspcqretpegaeak
    pwyepiylggvfqlekgdrlsaeinrpdyldfaesgqvyfgiialtsenlyfq
    

    Sequence, based on observed residues (ATOM records): (download)
    >5yoyA (A:)
    rtpsdkpvahvvanpqaegqlqwlnrranallangvelrdnqlvvpseglyliysqvlfk
    gqgcpsthvllthtisriavsyqtkvnllsaikspcqretpegaeakpwyepiylggvfq
    lekgdrlsaeinrpdyldfaesgqvyfgiialts
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >5yoyB (B:)
    dykddddkvrsssrtpsdkpvahvvanpqaegqlqwlnrranallangvelrdnqlvvps
    eglyliysqvlfkgqgcpsthvllthtisriavsyqtkvnllsaikspcqretpegaeak
    pwyepiylggvfqlekgdrlsaeinrpdyldfaesgqvyfgiialtsenlyfq
    

    Sequence, based on observed residues (ATOM records): (download)
    >5yoyB (B:)
    rtpsdkpvahvvanpqaegqlqwlnrranallangvelrdnqlvvpseglyliysqvlfk
    gqgcpsthvllthtisriavsyqtkvnllsaikspcqretpegaeakpwyepiylggvfq
    lekgdrlsaeinrpdyldfaesgqvyfgiialts
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >5yoyC (C:)
    dykddddkvrsssrtpsdkpvahvvanpqaegqlqwlnrranallangvelrdnqlvvps
    eglyliysqvlfkgqgcpsthvllthtisriavsyqtkvnllsaikspcqretpegaeak
    pwyepiylggvfqlekgdrlsaeinrpdyldfaesgqvyfgiialtsenlyfq
    

    Sequence, based on observed residues (ATOM records): (download)
    >5yoyC (C:)
    rtpsdkpvahvvanpqaegqlqwlnrranallangvelrdnqlvvpseglyliysqvlfk
    gqgcpsthvllthtisriavsyqtkvnllsaikspcqretpegaeakpwyepiylggvfq
    lekgdrlsaeinrpdyldfaesgqvyfgiialts
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >5yoyD (D:)
    agseivltqspatlslspgeratlscrasqsvysylawyqqkpgqaprlliydasnratg
    iparfsgsgsgtdftltisslepedfavyycqqrsnwppftfgpgtkvdiktsenlyfq
    

    Sequence, based on observed residues (ATOM records): (download)
    >5yoyD (D:)
    eivltqspatlslspgeratlscrasqsvysylawyqqkpgqaprlliydasnratgipa
    rfsgsgsgtdftltisslepedfavyycqqrsnwppftfgpgtkvdik
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >5yoyE (E:)
    agseivltqspatlslspgeratlscrasqsvysylawyqqkpgqaprlliydasnratg
    iparfsgsgsgtdftltisslepedfavyycqqrsnwppftfgpgtkvdiktsenlyfq
    

    Sequence, based on observed residues (ATOM records): (download)
    >5yoyE (E:)
    eivltqspatlslspgeratlscrasqsvysylawyqqkpgqaprlliydasnratgipa
    rfsgsgsgtdftltisslepedfavyycqqrsnwppftfgpgtkvdik
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >5yoyF (F:)
    agseivltqspatlslspgeratlscrasqsvysylawyqqkpgqaprlliydasnratg
    iparfsgsgsgtdftltisslepedfavyycqqrsnwppftfgpgtkvdiktsenlyfq
    

    Sequence, based on observed residues (ATOM records): (download)
    >5yoyF (F:)
    eivltqspatlslspgeratlscrasqsvysylawyqqkpgqaprlliydasnratgipa
    rfsgsgsgtdftltisslepedfavyycqqrsnwppftfgpgtkvdik
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >5yoyG (G:)
    sklqvqlvesgggvvqpgrslrlscaasgfifssyamhwvrqapgnglewvafmsydgsn
    kkyadsvkgrftisrdnskntlylqmnslraedtavyycardrgiaaggnyyyygmdvwg
    qgttvtvss
    

    Sequence, based on observed residues (ATOM records): (download)
    >5yoyG (G:)
    qvqlvesgggvvqpgrslrlscaasgfifssyamhwvrqapgnglewvafmsydgsnkky
    adsvkgrftisrdnskntlylqmnslraedtavyycardrgiaaggnyyyygmdvwgqgt
    tvtvss
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >5yoyH (H:)
    sklqvqlvesgggvvqpgrslrlscaasgfifssyamhwvrqapgnglewvafmsydgsn
    kkyadsvkgrftisrdnskntlylqmnslraedtavyycardrgiaaggnyyyygmdvwg
    qgttvtvss
    

    Sequence, based on observed residues (ATOM records): (download)
    >5yoyH (H:)
    qvqlvesgggvvqpgrslrlscaasgfifssyamhwvrqapgnglewvafmsydgsnkky
    adsvkgrftisrdnskntlylqmnslraedtavyycardrgiaaggnyyyygmdvwgqgt
    tvtvss
    

  • Chain 'I':
    Sequence, based on SEQRES records: (download)
    >5yoyI (I:)
    sklqvqlvesgggvvqpgrslrlscaasgfifssyamhwvrqapgnglewvafmsydgsn
    kkyadsvkgrftisrdnskntlylqmnslraedtavyycardrgiaaggnyyyygmdvwg
    qgttvtvss
    

    Sequence, based on observed residues (ATOM records): (download)
    >5yoyI (I:)
    qvqlvesgggvvqpgrslrlscaasgfifssyamhwvrqapgnglewvafmsydgsnkky
    adsvkgrftisrdnskntlylqmnslraedtavyycardrgiaaggnyyyygmdvwgqgt
    tvtvs
    

  • Chain 'J':
    Sequence, based on SEQRES records: (download)
    >5yoyJ (J:)
    dykddddkvrsssrtpsdkpvahvvanpqaegqlqwlnrranallangvelrdnqlvvps
    eglyliysqvlfkgqgcpsthvllthtisriavsyqtkvnllsaikspcqretpegaeak
    pwyepiylggvfqlekgdrlsaeinrpdyldfaesgqvyfgiialtsenlyfq
    

    Sequence, based on observed residues (ATOM records): (download)
    >5yoyJ (J:)
    rtpsdkpvahvvanpqaegqlqwlnrranallangvelrdnqlvvpseglyliysqvlfk
    gqgcpsthvllthtisriavsyqtkvnllsaikspcqretpegaeakpwyepiylggvfq
    lekgdrlsaeinrpdyldfaesgqvyfgiialt
    

  • Chain 'K':
    Sequence, based on SEQRES records: (download)
    >5yoyK (K:)
    dykddddkvrsssrtpsdkpvahvvanpqaegqlqwlnrranallangvelrdnqlvvps
    eglyliysqvlfkgqgcpsthvllthtisriavsyqtkvnllsaikspcqretpegaeak
    pwyepiylggvfqlekgdrlsaeinrpdyldfaesgqvyfgiialtsenlyfq
    

    Sequence, based on observed residues (ATOM records): (download)
    >5yoyK (K:)
    rtpsdkpvahvvanpqaegqlqwlnrranallangvelrdnqlvvpseglyliysqvlfk
    gqgcpsthvllthtisriavsyqtkvnllsaikspcqretpegaeakpwyepiylggvfq
    lekgdrlsaeinrpdyldfaesgqvyfgiialt
    

  • Chain 'L':
    Sequence, based on SEQRES records: (download)
    >5yoyL (L:)
    dykddddkvrsssrtpsdkpvahvvanpqaegqlqwlnrranallangvelrdnqlvvps
    eglyliysqvlfkgqgcpsthvllthtisriavsyqtkvnllsaikspcqretpegaeak
    pwyepiylggvfqlekgdrlsaeinrpdyldfaesgqvyfgiialtsenlyfq
    

    Sequence, based on observed residues (ATOM records): (download)
    >5yoyL (L:)
    rtpsdkpvahvvanpqaegqlqwlnrranallangvelrdnqlvvpseglyliysqvlfk
    gqgcpsthvllthtisriavsyqtkvnllsaikspcqretpegaeakpwyepiylggvfq
    lekgdrlsaeinrpdyldfaesgqvyfgiialt
    

  • Chain 'M':
    Sequence, based on SEQRES records: (download)
    >5yoyM (M:)
    agseivltqspatlslspgeratlscrasqsvysylawyqqkpgqaprlliydasnratg
    iparfsgsgsgtdftltisslepedfavyycqqrsnwppftfgpgtkvdiktsenlyfq
    

    Sequence, based on observed residues (ATOM records): (download)
    >5yoyM (M:)
    eivltqspatlslspgeratlscrasqsvysylawyqqkpgqaprlliydasnratgipa
    rfsgsgsgtdftltisslepedfavyycqqrsnwppftfgpgtkvdik
    

  • Chain 'N':
    Sequence, based on SEQRES records: (download)
    >5yoyN (N:)
    agseivltqspatlslspgeratlscrasqsvysylawyqqkpgqaprlliydasnratg
    iparfsgsgsgtdftltisslepedfavyycqqrsnwppftfgpgtkvdiktsenlyfq
    

    Sequence, based on observed residues (ATOM records): (download)
    >5yoyN (N:)
    eivltqspatlslspgeratlscrasqsvysylawyqqkpgqaprlliydasnratgipa
    rfsgsgsgtdftltisslepedfavyycqqrsnwppftfgpgtkvdik
    

  • Chain 'O':
    Sequence, based on SEQRES records: (download)
    >5yoyO (O:)
    agseivltqspatlslspgeratlscrasqsvysylawyqqkpgqaprlliydasnratg
    iparfsgsgsgtdftltisslepedfavyycqqrsnwppftfgpgtkvdiktsenlyfq
    

    Sequence, based on observed residues (ATOM records): (download)
    >5yoyO (O:)
    eivltqspatlslspgeratlscrasqsvysylawyqqkpgqaprlliydasnratgipa
    rfsgsgsgtdftltisslepedfavyycqqrsnwppftfgpgtkvdik
    

  • Chain 'P':
    Sequence, based on SEQRES records: (download)
    >5yoyP (P:)
    sklqvqlvesgggvvqpgrslrlscaasgfifssyamhwvrqapgnglewvafmsydgsn
    kkyadsvkgrftisrdnskntlylqmnslraedtavyycardrgiaaggnyyyygmdvwg
    qgttvtvss
    

    Sequence, based on observed residues (ATOM records): (download)
    >5yoyP (P:)
    qvqlvesgggvvqpgrslrlscaasgfifssyamhwvrqapgnglewvafmsydgsnkky
    adsvkgrftisrdnskntlylqmnslraedtavyycardrgiaaggnyyyygmdvwgqgt
    tvtvss
    

  • Chain 'Q':
    Sequence, based on SEQRES records: (download)
    >5yoyQ (Q:)
    sklqvqlvesgggvvqpgrslrlscaasgfifssyamhwvrqapgnglewvafmsydgsn
    kkyadsvkgrftisrdnskntlylqmnslraedtavyycardrgiaaggnyyyygmdvwg
    qgttvtvss
    

    Sequence, based on observed residues (ATOM records): (download)
    >5yoyQ (Q:)
    qvqlvesgggvvqpgrslrlscaasgfifssyamhwvrqapgnglewvafmsydgsnkky
    adsvkgrftisrdnskntlylqmnslraedtavyycardrgiaaggnyyyygmdvwgqgt
    tvtvss
    

  • Chain 'R':
    Sequence, based on SEQRES records: (download)
    >5yoyR (R:)
    sklqvqlvesgggvvqpgrslrlscaasgfifssyamhwvrqapgnglewvafmsydgsn
    kkyadsvkgrftisrdnskntlylqmnslraedtavyycardrgiaaggnyyyygmdvwg
    qgttvtvss
    

    Sequence, based on observed residues (ATOM records): (download)
    >5yoyR (R:)
    qvqlvesgggvvqpgrslrlscaasgfifssyamhwvrqapgnglewvafmsydgsnkky
    adsvkgrftisrdnskntlylqmnslraedtavyycardrgiaaggnyyyygmdvwgqgt
    tvtvss