Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 2369 |
| PDBID: | 6JBT |
| Chains: | HL_F |
| Organism: | Homo sapiens, Mus musculus |
| Method: | XRD |
| Resolution (Å): | 2.47 |
| Reference: | 10.1080/19420862.2019.1596513 |
| Antibody | |
| Antibody: | toripalimab Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | Toripalimab(Approved) |
| Antigen | |
| Antigen: | Programmed cell death protein 1 (PD-1) |
| Antigen mutation: | No |
| Durg Target: | Q15116 |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >6JBT_H|Chain B[auth H]|Heavy chain|Mus musculus (10090) QGQLVQSGAEVKKPGASVKVSCKASGYTFTDYEMHWVRQAPIHGLEWIGVIESETGGTAYNQKFKGRVTITADKSTSTAYMELSSLRSEDTAVYYCAREGITTVATTYYWYFDVWGQGTTVTVSSASTKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRV |
Light Chain: L
Mutation: NULL
| >6JBT_L|Chain C[auth L]|Light chain|Mus musculus (10090) DVVMTQSPLSLPVTLGQPASISCRSSQSIVHSNGNTYLEWYLQKPGQSPQLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCFQGSHVPLTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: F
Mutation: NULL
| >6JBT_F|Chain A[auth F]|Programmed cell death protein 1|Homo sapiens (9606) MPGWFLDSPDRPWNPPTFSPALLVVTEGDNATFTCSFSNTSESFVLNWYRMSPSNQTDKLAAFPEDRSQPGQDCRFRVTQLPNGRDFHMSVVRARRNDSGTYLCGAISLAPKAQIKESLRAELRVTERRAEVPTAHPSPSPRPAGQFQTLVHHHHHH |
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: GLU33 HIS35 TRP47 VAL50 GLU52 GLU54 THR55 GLY57 THR58 ALA59 GLU99 GLY100 ILE101 THR102 THR103 VAL104 TYR108 TYR109 TRP110 TYR111 L: HIS31 SER32 ASN33 TYR37 GLY96 SER97 HIS98 VAL99 LEU101 F: PRO12 TRP13 THR40 SER41 SER43 VAL45 ASN47 TYR49 LYS59 ILE107 LEU109 ALA110 PRO111 LYS112 ALA113 GLN114 ILE115 LYS116 GLU117 |
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)
