Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1946 |
| PDBID: | 5X8L |
| Chains: | JO_E |
| Organism: | Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 3.10 |
| Reference: | 10.1038/s41598-017-06002-8 |
| Antibody | |
| Antibody: | atezolizumab Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | Atezolizumab(Approved) |
| Antigen | |
| Antigen: | Programmed cell death 1 ligand 1 (PD-L1) |
| Antigen mutation: | Yes |
| Durg Target: | Q9NZQ7 |
Sequence information
Antibody
Heavy Chain: J
Mutation: NULL
| >5X8L_J|Chain C[auth F], F[auth G], I[auth H], L[auth J], O[auth S]|atezolizumab heavy chain|Homo sapiens (9606) EVQLVESGGGLVQPGGSLRLSCAASGFTFSDSWIHWVRQAPGKGLEWVAWISPYGGSTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARRHWPGGFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHHHHHH |
Light Chain: O
Mutation: NULL
| >5X8L_O|Chain B[auth K], E[auth L], H[auth M], K[auth N], N[auth O]|atezolizumab light chain|Homo sapiens (9606) DIQMTQSPSSLSASVGDRVTITCRASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQYLYHPATFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: E
Mutation: Q30E
| >5X8L_E|Chain A, D[auth B], G[auth C], J[auth D], M[auth E]|Programmed cell death 1 ligand 1|Homo sapiens (9606) AFTVTVPKDLYVVEYGSNMTIECKFPVEKELDLAALIVYWEMEDKNIIQFVHGEEDLKVQHSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNAPYHHHHHH |
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)
| O: GLN27 ALA32 PHE53 TYR91 LEU92 TYR93 HIS94 PRO95 J: SER30 ASP31 SER32 TRP33 TRP50 SER52 PRO53 TYR54 GLY55 SER57 THR58 TYR59 THR74 ARG99 TRP101 PRO102 E: ALA18 PHE19 ASP49 ALA51 ALA52 ILE54 TYR56 GLU58 MET59 GLU60 ASP61 LYS62 ASN63 GLN66 VAL68 HIS69 VAL76 VAL111 ARG113 MET115 SER117 TYR118 GLY119 GLY120 ALA121 ASP122 TYR123 ARG125 |
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)
