Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5833 |
| PDBID: | 8AS0 |
| Chains: | BC_A |
| Organism: | Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 3.50 |
| Reference: | 10.1002/pro.4486 |
| Antibody | |
| Antibody: | D12 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Human programmed cell death protein 1 (PD-1) |
| Antigen mutation: | No |
| Durg Target: | Q15116 |
Sequence information
Antibody
Heavy Chain: B
Mutation: NULL
| >8AS0_B|Chain B, E, H, K, N, Q, T, W|D12 antibody heavy chain, Fab fragment|Homo sapiens (9606) EVQLLESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGSGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKSYNHPMFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH |
Light Chain: C
Mutation: NULL
| >8AS0_C|Chain A[auth C], D, G, J, M, P, S, V|D12 antibody light chain, Fab fragment|Homo sapiens (9606) DIQMTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQDYGLPFTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: A
Mutation: NULL
| >8AS0_A|Chain C[auth A], F, I, L, O, R, U[auth X], X[auth Y]|Programmed cell death protein 1|Homo sapiens (9606) FLDSPDRPWNPPTFSPALLVVTEGDNATFTCSFSNTSESFVLNWYRMSPSNQTDKLAAFPEDRSQPGQDCRFRVTQLPNGRDFHMSVVRARRNDSGTYLCGAISLAPKAQIKESLRAELRVTERRAEVPTAHPSPSPRPAGQFQTLVGLNDIFEAQKIEWHEHHHHHH |
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)
| C: ASP1 ASP91 TYR92 GLY93 LEU94 PRO95 PHE96 B: SER30 SER31 TYR32 ALA33 SER52 GLY53 SER54 GLY56 SER57 THR58 TYR59 ASP62 LYS65 ASN74 SER75 TYR100 ASN101 HIS102 MET104 A: ARG30 PRO31 TRP32 ASN33 PRO34 THR36 MET70 ASN74 THR76 LYS131 GLN133 ILE134 LYS135 GLU136 SER137 LEU138 ARG139 |
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)
