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 2.06 freeze date was dated 2016-10-26, with a file datestamp of 2016-10-21.
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]
    Database cross-references and differences (RAF-indexed):
    • PDB 5B8C (0-End)
    Domains in SCOPe 2.06: d5b8ca_
  • Chain 'B':
    Compound: Pembrolizumab heavy chain variable region (PemVH)
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 5B8C (0-119)
    Domains in SCOPe 2.06: 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 2.06: d5b8cc1, d5b8cc2
  • Chain 'D':
    Compound: Pembrolizumab light chain variable region (PemVL)
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 5B8C (0-End)
    Domains in SCOPe 2.06: d5b8cd_
  • Chain 'E':
    Compound: Pembrolizumab heavy chain variable region (PemVH)
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 5B8C (0-119)
    Domains in SCOPe 2.06: 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 2.06: d5b8cf1, d5b8cf2
  • Chain 'G':
    Compound: Pembrolizumab light chain variable region (PemVL)
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 5B8C (0-End)
    Domains in SCOPe 2.06: d5b8cg_
  • Chain 'H':
    Compound: Pembrolizumab heavy chain variable region (PemVH)
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 5B8C (0-119)
    Domains in SCOPe 2.06: 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 2.06: d5b8ci1, d5b8ci2
  • Chain 'J':
    Compound: Pembrolizumab light chain variable region (PemVL)
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 5B8C (0-End)
    Domains in SCOPe 2.06: d5b8cj_
  • Chain 'K':
    Compound: Pembrolizumab heavy chain variable region (PemVH)
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 5B8C (0-119)
    Domains in SCOPe 2.06: 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 2.06: 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