Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1929 |
| PDBID: | 5WT9 |
| Chains: | HL_G |
| Organism: | Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 2.40 |
| Reference: | 10.1038/ncomms14369 |
| 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: H
Mutation: NULL
| >5WT9_H|Chain A[auth H]|Heavy Chain of Nivolumab|Homo sapiens (9606) QVQLVESGGGVVQPGRSLRLDCKASGITFSNSGMHWVRQAPGKGLEWVAVIWYDGSKRYYADSVKGRFTISRDNSKNTLFLQMNSLRAEDTAVYYCATNDDYWGQGTLVTVSSASTKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVESKYGPPCP |
Light Chain: L
Mutation: NULL
| >5WT9_L|Chain B[auth L]|Light Chain of Nivolumab|Homo sapiens (9606) STGEIVLTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQSSNWPRTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: G
Mutation: NULL
| >5WT9_G|Chain C[auth G]|Programmed cell death protein 1|Homo sapiens (9606) MQIPQAPWPVVWAVLQLGWRPGWFLDSPDRPWNPPTFSPALLVVTEGDNATFTCSFSNTSESFVLNWYRMSPSNQTDKLAAFPEDRSQPGQDCRFRVTQLPNGRDFHMSVVRARRNDSGTYLCGAISLAPKAQIKESLRAELRVTERRAEVPTAHPSPSPRPAGQFQHHHHHH |
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)
| H: GLN1 VAL2 GLY26 ILE27 THR28 SER30 ASN31 SER32 GLY33 VAL50 TRP52 TYR53 LYS57 ASN99 ASP100 ASP101 TYR102 L: TYR32 ALA34 TYR36 LEU46 TYR49 ASP50 ARG54 ALA55 THR56 GLN89 SER91 SER92 TRP94 ARG96 G: LEU25 ASP26 SER27 PRO28 ASP29 ARG30 PRO31 THR59 SER60 GLU61 SER62 LEU128 ALA129 PRO130 LYS131 ALA132 |
2、We defined interacting paratope-epitope residues by a distance cutoff of < 5Å . Two amino acids are considered as interacting residues if they have at least one atom within a distance of 5 Å from any atom.
Interacting residues (Atom distance based)
