Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5295 |
| PDBID: | 7VUX |
| Chains: | HL_A |
| Organism: | Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 1.64 |
| Reference: | 10.1080/19420862.2022.2044435 |
| Antibody | |
| Antibody: | 609A Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Programmed cell death protein 1 (PD1) |
| Antigen mutation: | No |
| Durg Target: | Q15116 |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >7VUX_H|Chain B[auth H]|Heavy chain of Fab fragment|Homo sapiens (9606) EVKLVESGGGLVQPGGSLRLSCAASGFAFSSYDMSWVRQAPGKRLEWVATISGGGRYTYYPDTVKGRFTISRDNAKNSHYLQMNSLRAEDTAVYFCASPYGGYFDVWGQGTLVTVSSASTKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVE |
Light Chain: L
Mutation: NULL
| >7VUX_L|Chain C[auth L]|Light chain of Fab fragment|Homo sapiens (9606) EIVLTQSPATLSLSPGERATLSCRASQSISNFLHWYQQKPGQAPRLLIKYASQSISGIPARFSGSGSGTDFTLTISSLEPEDFAVYFCQQSNSWPHTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: A
Mutation: NULL
| >7VUX_A|Chain A|Programmed cell death protein 1|Homo sapiens (9606) MWNPPTFSPALLVVTEGDNATFTCSFSNTSESFVLNWYRMSPSNQTDKLAAFPEDRSQPGQDSRFRVTQLPNGRDFHMSVVRARRNDSGTYLCGAISLAPKAQIKESLRAELRVTERRAEVPTAHPSPSPENLYFQ |
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: VAL2 PHE27 SER31 TYR32 ASP33 SER52 TYR57 TYR59 SER98 PRO99 TYR100 GLY101 GLY102 TYR103 ASP105 VAL106 L: ASN31 PHE32 LYS49 TYR50 GLN53 ILE55 SER56 SER91 ASN92 SER93 TRP94 HIS96 A: THR59 SER60 GLU61 SER62 PHE63 VAL64 LYS78 ALA81 PRO83 GLU84 ASP85 ARG86 SER87 GLN88 PRO89 ILE126 LEU128 ALA129 PRO130 LYS131 ALA132 GLN133 ILE134 |
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)
