Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1479 |
| PDBID: | 5JYL |
| Chains: | D_C |
| Organism: | Homo sapiens, Mus musculus |
| Method: | XRD |
| Resolution (Å): | 2.55 |
| Reference: | 10.1038/srep39518 |
| Antibody | |
| Antibody: | TSP7 scFv |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Cadherin-3 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: D
Mutation: NULL
| >5JYL_D|Chain B, D|scFv TSP7|Mus musculus (10090) QVQLQESGPELVKPGASVKMSCKASGYSFTAYNMHWVKQSHGKSLEWIGFIDPYSGIITYNQTFKGKATLTVDKSSSTAYMQLNSLTSEDSAVYYCARRGYYDGGFDYWGQGTTLTVSSSAGGGGSGGGGSGGGGSDIDIQMTQTTSSLSASLGDRVTISCRASQDITNYLNWYQQKPDGTVKLLIYYTSRLHSGVPSRFSGSGSGTDYSLTISNLEQEDIATYFCQQDSKHPRTFGGGTKLEIKSAHHHHHH |
Antigen
Chain: C
Mutation: NULL
| >5JYL_C|Chain A, C|Cadherin-3|Homo sapiens (9606) MDWVVAPISVPENGKGPFPQRLNQLKSNKDRDTKIFYSITGPGADSPPEGVFAVEKETGWLLLNKPLDREEIAKYELFGHAVSENGASVEDPMNISIIVTD |
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)
| Chain residues position delta_SASA
: residuesposition D: THR30 ALA31 TYR32 ASN33 HIS35 PHE50 ASP52 TYR54 SER55 ILE57 THR59 ARG99 GLY100 TYR101 TYR102 ASP103 GLY104 TYR170 ARG191 ASP229 SER230 HIS232 ARG234 C: GLN23 LYS25 SER26 ASN27 LYS28 ASP29 ARG30 ASP31 THR32 SER82 ASN84 ALA86 SER87 VAL88 GLU89 ASP90 |
2、We defined interacting paratope-epitope residues by a distance cutoff of < 6 Å . Two amino acids are considered as interacting residues if they have at least one atom within a distance of 6 Å from any atom.
Interacting residues (Atom distance based)
