Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 2359 |
| PDBID: | 6J15 |
| Chains: | AB_C |
| Organism: | Homo sapiens, Mus musculus |
| Method: | XRD |
| Resolution (Å): | 2.60 |
| Reference: | 10.1016/j.isci.2019.03.017 |
| Antibody | |
| Antibody: | GY-5 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Programmed cell death protein 1 (PD-1) |
| Antigen mutation: | No |
| Durg Target: | Q15116 |
Sequence information
Antibody
Heavy Chain: A
Mutation: NULL
| >6J15_A|Chain C[auth A], E[auth H]|GY-5 heavy chain Fab|Mus musculus (10090) QVQLQQSGPELVRPGVSVKISCKGSGHTFTDYALHWVRQSHVKSLEWIGVISSYNGITNYNQRFKGKATMTVDKSSSTAYLELARLTSEDSAIYYCSREEWDVFYYFDYWGQGTTLTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIET |
Light Chain: B
Mutation: NULL
| >6J15_B|Chain D[auth B], F[auth L]|GY-5 light chain Fab|Mus musculus (10090) DIMLTQSPLSLPVSLGDQASISCRSSQGIVHSDGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFILKISRVEAEDLGVYYCFQGSHVPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKNFNR |
Antigen
Chain: C
Mutation: NULL
| >6J15_C|Chain A[auth C], B[auth D]|Programmed cell death protein 1|Homo sapiens (9606) DGIQWNPPTFSPALLVVTEGDNATFTCSFSNTSESFVLNWYRMSPSNQTDKLAAFPEDRSQPGQDCRFRVTQLPNGRDFHMSVVRARRNDSGTYLCGAISLAPKAQIKESLRAELRVTER |
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)
| A: ALA31 VAL48 SER50 TYR52 ASN53 ILE55 THR56 ASN57 GLU97 TRP99 ASP100 VAL101 PHE102 TYR103 TYR104 B: VAL30 HIS31 SER32 ASP33 GLY34 TYR37 GLY96 SER97 HIS98 VAL99 TYR101 C: ILE30 GLN31 TRP32 THR59 SER60 SER62 PHE63 VAL64 LYS78 ILE126 SER127 LEU128 ALA129 PRO130 LYS131 ALA132 GLN133 ILE134 LYS135 |
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)
