Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1372 |
| PDBID: | 5GGS |
| Chains: | AB_Z |
| Organism: | Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 2.00 |
| Reference: | 10.1038/ncomms13354 |
| Antibody | |
| Antibody: | pembrolizumab Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | Pembrolizumab(Approved) |
| Antigen | |
| Antigen: | Programmed cell death protein 1 |
| Antigen mutation: | No |
| Durg Target: | Q15116 |
Sequence information
Antibody
Heavy Chain: A
Mutation: NULL
| >5GGS_A|Chain A, C|heavy chain|Homo sapiens (9606) QVQLVQSGVEVKKPGASVKVSCKASGYTFTNYYMYWVRQAPGQGLEWMGGINPSNGGTNFNEKFKNRVTLTTDSSTTTAYMELKSLQFDDTAVYYCARRDYRFDMGFDYWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHHHHHH |
Light Chain: B
Mutation: NULL
| >5GGS_B|Chain B, D|light chain|Homo sapiens (9606) EIVLTQSPATLSLSPGERATLSCRASKGVSTSGYSYLHWYQQKPGQAPRLLIYLASYLESGVPARFSGSGSGTDFTLTISSLEPEDFAVYYCQHSRDLPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: Z
Mutation: NULL
| >5GGS_Z|Chain E[auth Y], F[auth Z]|Programmed cell death protein 1|Homo sapiens (9606) DSPDRPWNPPTFSPALLVVTEGDNATFTCSFSNTSESFVLNWYRMSPSNQTDKLAAFPEDRSQPGQDSRFRVTQLPNGRDFHMSVVRARRNDSGTYLCGAISLAPKAQIKESLRAELRVTERR |
Interaction
1、Solvent accessible surface areas (SASA) were calculated (Naccess V2.1.1) for each residue in antibody and antigen, respectively. The residues with SASA loss in binding of more than 1Å2 were classified as interacting residues.
Interacting residues (ΔSASA based)
| Chain residues position delta_SASA
: residuesposition A: THR30 TYR33 TYR35 GLY50 ILE51 ASN52 SER54 ASN55 GLY57 THR58 ASN59 ARG99 ASP100 TYR101 ARG102 PHE103 ASP104 MET105 ASP108 B: THR31 SER32 GLY33 TYR34 TYR36 TYR53 LEU54 TYR57 GLU59 SER60 SER95 ARG96 ASP97 LEU98 LEU100 Z: SER60 SER62 PHE63 VAL64 ASN66 TYR68 GLN75 THR76 ASP77 LYS78 ALA81 PHE82 PRO83 GLU84 ASP85 ARG86 SER87 GLN88 PRO89 GLY90 ILE126 LEU128 ALA129 LYS131 ALA132 ILE134 |
2、We defined interacting paratope-epitope residues by a distance cutoff of < 6 Å . Two amino acids are considered as interacting residues if they have at least one atom within a distance of 6 Å from any atom.
Interacting residues (Atom distance based)
