Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1981 |
| PDBID: | 5YOY |
| Chains: | GD_B |
| Organism: | Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 2.73 |
| Reference: | 10.1002/pro.3407 |
| Antibody | |
| Antibody: | Golimumab Fv |
| Antibody mutation: | No |
| INN (Clinical Trial): | Golimumab(Approved) |
| Antigen | |
| Antigen: | Tumor necrosis factor |
| Antigen mutation: | No |
| Durg Target: | P01375 |
Sequence information
Antibody
Heavy Chain: G
Mutation: NULL
| >5YOY_G|Chain G, H, I, P, Q, R|Golimumab heavy chain variable region|Homo sapiens (9606) SKLQVQLVESGGGVVQPGRSLRLSCAASGFIFSSYAMHWVRQAPGNGLEWVAFMSYDGSNKKYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARDRGIAAGGNYYYYGMDVWGQGTTVTVSS |
Light Chain: D
Mutation: NULL
| >5YOY_D|Chain D, E, F, M, N, O|Golimumab light chain variable region|Homo sapiens (9606) AGSEIVLTQSPATLSLSPGERATLSCRASQSVYSYLAWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQRSNWPPFTFGPGTKVDIKTSENLYFQ |
Antigen
Chain: B
Mutation: NULL
| >5YOY_B|Chain A, B, C, J, K, L|Tumor necrosis factor|Homo sapiens (9606) DYKDDDDKVRSSSRTPSDKPVAHVVANPQAEGQLQWLNRRANALLANGVELRDNQLVVPSEGLYLIYSQVLFKGQGCPSTHVLLTHTISRIAVSYQTKVNLLSAIKSPCQRETPEGAEAKPWYEPIYLGGVFQLEKGDRLSAEINRPDYLDFAESGQVYFGIIALTSENLYFQ |
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)
| D: GLU1 ILE2 GLN27 TYR30 TYR32 TRP94 G: ILE28 SER30 SER31 TYR32 TYR53 ASN57 ARG98 ARG100 GLY101 ILE102 ALA103 ALA104 GLY105 GLY106 ASN107 TYR108 TYR109 TYR110 TYR111 ASP114 B: ALA22 GLU23 GLY24 LYS65 GLY66 GLN67 GLY68 CYS69 PRO70 SER71 THR72 GLU104 THR105 PRO106 GLU107 GLY108 ALA109 GLU110 ALA111 LYS112 PRO113 ARG138 PRO139 ASP140 TYR141 LEU142 ASP143 PHE144 |
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)
