Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1371 |
| PDBID: | 5GGR |
| Chains: | AB_Y |
| Organism: | Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 3.30 |
| Reference: | 10.1038/ncomms13354 |
| Antibody | |
| Antibody: | nivolumab Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | Nivolumab(Approved) |
| Antigen | |
| Antigen: | Programmed cell death protein 1 |
| Antigen mutation: | No |
| Durg Target: | Q15116 |
Sequence information
Antibody
Heavy Chain: A
Mutation: NULL
| >5GGR_A|Chain A, C[auth H]|heavy chain|Homo sapiens (9606) QVQLVESGGGVVQPGRSLRLDCKASGITFSNSGMHWVRQAPGKGLEWVAVIWYDGSKRYYADSVKGRFTISRDNSKNTLFLQMNSLRAEDTAVYYCATNDDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHHHHHH |
Light Chain: B
Mutation: NULL
| >5GGR_B|Chain B, D[auth L]|light chain|Homo sapiens (9606) EIVLTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQSSNWPRTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: Y
Mutation: NULL
| >5GGR_Y|Chain E[auth Y], F[auth Z]|Programmed cell death protein 1|Homo sapiens (9606) DSPDRPWNPPTFSPALLVVTEGDNATFTCSFSNTSESFVLNWYRMSPSNQTDKLAAFPEDRSQPGQDSRFRVTQLPNGRDFHMSVVRARRNDSGTYLCGAISLAPKAQIKESLRAELRVTERRAE |
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: ILE27 THR28 ASN31 SER32 GLY33 VAL50 TRP52 TYR53 ASN99 ASP100 ASP101 TYR102 B: LEU46 TYR49 ASP50 ALA55 THR56 SER91 TRP94 ARG96 Y: SER27 PRO28 ASP29 ARG30 PRO31 SER60 GLU61 ILE126 SER127 LEU128 ALA129 PRO130 LYS131 ALA132 GLN133 |
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)
