Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5907 |
| PDBID: | 8CXC |
| Chains: | A_M |
| Organism: | Mus musculus, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 4.31 |
| Reference: | 10.3389/fddsv.2023.1216516 |
| Antibody | |
| Antibody: | Amatuximab scFv |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Human mesothelin |
| Antigen mutation: | No |
| Durg Target: | Q13421; Q13421; |
Sequence information
Antibody
Chain: A
Mutation: NULL
| >8CXC_A|Chain D[auth A]|scFv Amatuximab|Mus musculus (10090) DIELTQSPAIMSASPGEKVTMTCSASSSVSYMHWYQQKSGTSPKRWIYDTSKLASGVPGRFSGSGSGNSYSLTISSVEAEDDATYYCQQWSKHPLTFGSGTKVEIKGSGLVPRGSGSVQLQQSGPELEKPGASVKISCKASGYSFTGYTMNWVKQSHGKSLEWIGLITPYNGASSYNQKFRGKATLTVDKSSSTAYMDLLSLTSEDSAVYFCARGGYDGRGFDYWGSGTPVTVS |
Antigen
Chain: M
Mutation: NULL
| >8CXC_M|Chain C[auth M]|Mesothelin, cleaved form|Homo sapiens (9606) EVEKTACPSGKKAREIDESLIFYKKWELEACVDAALLATQMDRVNAIPFTYEQLDVLKHKLDELYPQGYPESVIQHLGYLFLKMSPEDIRKWNVTSLETLKALLEVNKGHEMSPQAPRRPLPQVATLIDRFVKGRGQLDKDTLDTLTAFYPGYLCSLSPEELSSVPPSSIWAVRPQDLDTCDPRQLDVLYPKARLAFQNMNGSEYFVKIQSFLGGAPTEDLKALSQQNVSMDLATFMKLRTDAVLPLTVAEVQKLLGPHVEGLKAEERHRPVRDWILRQRQDDLDTLGLGLQGGIPNGYLVLDLSMQEALGSGLNDIFEAQKIEWHE |
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)
| A: SER31 TYR32 ASP50 TRP91 SER92 LYS93 HIS94 PRO95 LEU96 THR147 GLY148 TYR149 THR150 TRP164 LEU167 THR169 TYR171 ASN172 ALA174 SER175 SER176 LYS191 SER192 GLY217 TYR218 ASP219 GLY220 M: PRO303 GLU313 SER314 ILE316 PHE317 TYR318 LYS319 LYS320 TRP321 GLU322 ASN340 ALA341 PRO343 PHE344 THR345 TYR346 GLU347 GLN348 TYR374 LEU377 VAL401 GLY404 GLU406 |
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)
