PDB entry 5b8c

View 5b8c on RCSB PDB site
Description: High resolution structure of the human PD-1 in complex with pembrolizumab Fv
Class: immune system
Keywords: antibody, IMMUNE SYSTEM
Deposited on 2016-06-14, released 2016-10-26
The last revision prior to the SCOPe 2.07 freeze date was dated 2017-10-18, with a file datestamp of 2017-10-13.
Experiment type: XRAY
Resolution: 2.15 Å
R-factor: N/A
AEROSPACI score: 0.27 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Pembrolizumab light chain variable region (PemVL)
    Species: Homo sapiens [TaxId:9606]
    Gene:
    Database cross-references and differences (RAF-indexed):
    • PDB 5B8C (0-End)
    Domains in SCOPe 2.07: d5b8ca_
  • Chain 'B':
    Compound: Pembrolizumab heavy chain variable region (PemVH)
    Species: Homo sapiens [TaxId:9606]
    Gene:
    Database cross-references and differences (RAF-indexed):
    • PDB 5B8C (0-119)
    Domains in SCOPe 2.07: d5b8cb_
  • Chain 'C':
    Compound: Programmed cell death protein 1
    Species: Homo sapiens [TaxId:9606]
    Gene: Pdcd1, Pd1
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q15116 (2-End)
      • expression tag (1)
      • engineered mutation (63)
    Domains in SCOPe 2.07: d5b8cc1, d5b8cc2
  • Chain 'D':
    Compound: Pembrolizumab light chain variable region (PemVL)
    Species: Homo sapiens [TaxId:9606]
    Gene:
    Database cross-references and differences (RAF-indexed):
    • PDB 5B8C (0-End)
    Domains in SCOPe 2.07: d5b8cd_
  • Chain 'E':
    Compound: Pembrolizumab heavy chain variable region (PemVH)
    Species: Homo sapiens [TaxId:9606]
    Gene:
    Database cross-references and differences (RAF-indexed):
    • PDB 5B8C (0-119)
    Domains in SCOPe 2.07: d5b8ce_
  • Chain 'F':
    Compound: Programmed cell death protein 1
    Species: Homo sapiens [TaxId:9606]
    Gene: Pdcd1, Pd1
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q15116 (2-End)
      • expression tag (1)
      • engineered mutation (63)
    Domains in SCOPe 2.07: d5b8cf1, d5b8cf2
  • Chain 'G':
    Compound: Pembrolizumab light chain variable region (PemVL)
    Species: Homo sapiens [TaxId:9606]
    Gene:
    Database cross-references and differences (RAF-indexed):
    • PDB 5B8C (0-End)
    Domains in SCOPe 2.07: d5b8cg_
  • Chain 'H':
    Compound: Pembrolizumab heavy chain variable region (PemVH)
    Species: Homo sapiens [TaxId:9606]
    Gene:
    Database cross-references and differences (RAF-indexed):
    • PDB 5B8C (0-119)
    Domains in SCOPe 2.07: d5b8ch_
  • Chain 'I':
    Compound: Programmed cell death protein 1
    Species: Homo sapiens [TaxId:9606]
    Gene: Pdcd1, Pd1
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q15116 (2-End)
      • expression tag (1)
      • engineered mutation (63)
    Domains in SCOPe 2.07: d5b8ci1, d5b8ci2
  • Chain 'J':
    Compound: Pembrolizumab light chain variable region (PemVL)
    Species: Homo sapiens [TaxId:9606]
    Gene:
    Database cross-references and differences (RAF-indexed):
    • PDB 5B8C (0-End)
    Domains in SCOPe 2.07: d5b8cj_
  • Chain 'K':
    Compound: Pembrolizumab heavy chain variable region (PemVH)
    Species: Homo sapiens [TaxId:9606]
    Gene:
    Database cross-references and differences (RAF-indexed):
    • PDB 5B8C (0-119)
    Domains in SCOPe 2.07: d5b8ck_
  • Chain 'L':
    Compound: Programmed cell death protein 1
    Species: Homo sapiens [TaxId:9606]
    Gene: Pdcd1, Pd1
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q15116 (2-End)
      • expression tag (1)
      • engineered mutation (63)
    Domains in SCOPe 2.07: d5b8cl1, d5b8cl2
  • Heterogens: HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >5b8cA (A:)
    eivltqspatlslspgeratlscraskgvstsgysylhwyqqkpgqaprlliylasyles
    gvparfsgsgsgtdftltisslepedfavyycqhsrdlpltfgggtkveiktsenlyfq
    

    Sequence, based on observed residues (ATOM records): (download)
    >5b8cA (A:)
    eivltqspatlslspgeratlscraskgvstsgysylhwyqqkpgqaprlliylasyles
    gvparfsgsgsgtdftltisslepedfavyycqhsrdlpltfgggtkveik
    

  • Chain 'B':
    Sequence; same for both SEQRES and ATOM records: (download)
    >5b8cB (B:)
    qvqlvqsgvevkkpgasvkvsckasgytftnyymywvrqapgqglewmgginpsnggtnf
    nekfknrvtlttdsstttaymelkslqfddtavyycarrdyrfdmgfdywgqgttvtvss
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >5b8cC (C:)
    gswnpptfspallvvtegdnatftcsfsntsesfvlnwyrmspsnqtdklaafpedrsqp
    gqdsrfrvtqlpngrdfhmsvvrarrndsgtylcgaislapkaqikeslraelrvterra
    evptahpspsptsenlyfq
    

    Sequence, based on observed residues (ATOM records): (download)
    >5b8cC (C:)
    swnpptfspallvvtegdnatftcsfsntsesfvlnwyrmspsnqtdklaafpedrsqpg
    qdsrfrvtqlpngrdfhmsvvrarrndsgtylcgaislapkaqikeslraelrvte
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >5b8cD (D:)
    eivltqspatlslspgeratlscraskgvstsgysylhwyqqkpgqaprlliylasyles
    gvparfsgsgsgtdftltisslepedfavyycqhsrdlpltfgggtkveiktsenlyfq
    

    Sequence, based on observed residues (ATOM records): (download)
    >5b8cD (D:)
    eivltqspatlslspgeratlscraskgvstsgysylhwyqqkpgqaprlliylasyles
    gvparfsgsgsgtdftltisslepedfavyycqhsrdlpltfgggtkveik
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >5b8cE (E:)
    qvqlvqsgvevkkpgasvkvsckasgytftnyymywvrqapgqglewmgginpsnggtnf
    nekfknrvtlttdsstttaymelkslqfddtavyycarrdyrfdmgfdywgqgttvtvss
    

    Sequence, based on observed residues (ATOM records): (download)
    >5b8cE (E:)
    qvqlvqsgvevkkpgasvkvsckasytftnyymywvrqapgqglewmgginpsnggtnfn
    ekfknrvtlttdsstttaymelkslqfddtavyycarrdyrfdmgfdywgqgttvtvss
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >5b8cF (F:)
    gswnpptfspallvvtegdnatftcsfsntsesfvlnwyrmspsnqtdklaafpedrsqp
    gqdsrfrvtqlpngrdfhmsvvrarrndsgtylcgaislapkaqikeslraelrvterra
    evptahpspsptsenlyfq
    

    Sequence, based on observed residues (ATOM records): (download)
    >5b8cF (F:)
    swnpptfspallvvtegdnatftcsfsntsesfvlnwyrmspsnqtdklaafpedrsqpg
    qdsrfrvtqlpngrdfhmsvvrarrndsgtylcgaislapkaqikeslraelrvte
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >5b8cG (G:)
    eivltqspatlslspgeratlscraskgvstsgysylhwyqqkpgqaprlliylasyles
    gvparfsgsgsgtdftltisslepedfavyycqhsrdlpltfgggtkveiktsenlyfq
    

    Sequence, based on observed residues (ATOM records): (download)
    >5b8cG (G:)
    eivltqspatlslspgeratlscraskgvstsgysylhwyqqkpgqaprlliylasyles
    gvparfsgsgsgtdftltisslepedfavyycqhsrdlpltfgggtkveik
    

  • Chain 'H':
    Sequence; same for both SEQRES and ATOM records: (download)
    >5b8cH (H:)
    qvqlvqsgvevkkpgasvkvsckasgytftnyymywvrqapgqglewmgginpsnggtnf
    nekfknrvtlttdsstttaymelkslqfddtavyycarrdyrfdmgfdywgqgttvtvss
    

  • Chain 'I':
    Sequence, based on SEQRES records: (download)
    >5b8cI (I:)
    gswnpptfspallvvtegdnatftcsfsntsesfvlnwyrmspsnqtdklaafpedrsqp
    gqdsrfrvtqlpngrdfhmsvvrarrndsgtylcgaislapkaqikeslraelrvterra
    evptahpspsptsenlyfq
    

    Sequence, based on observed residues (ATOM records): (download)
    >5b8cI (I:)
    swnpptfspallvvtegdnatftcsfsnsfvlnwyrmspsnqtdklaafpedrsqpgqds
    rfrvtqlpngrdfhmsvvrarrndsgtylcgaislapkaqikeslraelrvte
    

  • Chain 'J':
    Sequence, based on SEQRES records: (download)
    >5b8cJ (J:)
    eivltqspatlslspgeratlscraskgvstsgysylhwyqqkpgqaprlliylasyles
    gvparfsgsgsgtdftltisslepedfavyycqhsrdlpltfgggtkveiktsenlyfq
    

    Sequence, based on observed residues (ATOM records): (download)
    >5b8cJ (J:)
    eivltqspatlslspgeratlscraskgvstsgysylhwyqqkpgqaprlliylasyles
    gvparfsgsgsgtdftltisslepedfavyycqhsrdlpltfgggtkveik
    

  • Chain 'K':
    Sequence; same for both SEQRES and ATOM records: (download)
    >5b8cK (K:)
    qvqlvqsgvevkkpgasvkvsckasgytftnyymywvrqapgqglewmgginpsnggtnf
    nekfknrvtlttdsstttaymelkslqfddtavyycarrdyrfdmgfdywgqgttvtvss
    

  • Chain 'L':
    Sequence, based on SEQRES records: (download)
    >5b8cL (L:)
    gswnpptfspallvvtegdnatftcsfsntsesfvlnwyrmspsnqtdklaafpedrsqp
    gqdsrfrvtqlpngrdfhmsvvrarrndsgtylcgaislapkaqikeslraelrvterra
    evptahpspsptsenlyfq
    

    Sequence, based on observed residues (ATOM records): (download)
    >5b8cL (L:)
    swnpptfspallvvtegdnatftcsfsnsfvlnwyrmspsnqtdklaafpedrsqpgqds
    rfrvtqlpngrdfhmsvvrarrndsgtylcgaislapkaqikeslraelrvte