Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1481 |
| PDBID: | 5JYM |
| Chains: | D_C |
| Organism: | Homo sapiens, Mus musculus |
| Method: | XRD |
| Resolution (Å): | 2.45 |
| Reference: | 10.1038/srep39518 |
| Antibody | |
| Antibody: | TSP11 scFv |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Cadherin-3 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: D
Mutation: NULL
| >5JYM_D|Chain B, D|Antibody scFv TSP11|Mus musculus (10090) QVQLQQPGTELVKPGASVKLSCKASGYTFTRYWINWVKQRPQGGLEWIGNIYPGSNITNYNEKFKNKATLTVDTSSNTAYMQLSSLTSDDSAVYYCAREGIYDGYFPLFPYWGQGTLVTVSASAGGGGSGGGGSGGGGSDIENVLTQSPAIMAASPGEKVTMTCSASSSVSSGNFHWYQQKPGTSPKLWIYRTSNLASGVPARFSGSGSGTSYSLTISSMEAEDAATYYCQQWSGYPWTFGGGTKLEIKSAHHHHHH |
Antigen
Chain: C
Mutation: NULL
| >5JYM_C|Chain A, C|Cadherin-3|Homo sapiens (9606) DWVVAPISVPENGKGPFPQRLNQLKSNKDRDTKIFYSITGPGADSPPEGVFAVEKETGWLLLNKPLDREEIAKYELFGHAVSENGASVEDPMNISIIVTDQNDHKPKFTQDTFRGSVLEGVLPGTSVMQVTATDEDDAIYTYNGVVAYSIHSQEPKDPHDLMFTIHRSTGTISVISSGLDREKVPEYTLTIQATDMDGDGSTTTAVAVVEILD |
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: ARG31 TYR32 TRP33 TYR52 SER55 ASN56 ILE57 ASN59 ARG98 GLU99 TYR102 ASP103 GLY104 TYR105 PHE106 PRO107 VAL170 SER171 SER172 GLY173 ASN174 GLY210 TRP233 TYR236 C: GLY13 LYS14 PRO16 PHE17 PRO18 PHE35 TYR36 SER37 ILE38 ALA43 ASP44 SER45 PRO47 GLU48 GLY49 VAL50 PHE51 ALA52 VAL53 GLU54 LYS55 GLU56 LEU61 ASN63 LYS64 PRO65 GLU70 |
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)
