Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5906 |
| PDBID: | 8CXC |
| Chains: | HL_M |
| Organism: | Mus musculus, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 4.31 |
| Reference: | 10.3389/fddsv.2023.1216516 |
| Antibody | |
| Antibody: | 3F2 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Human mesothelin |
| Antigen mutation: | No |
| Durg Target: | Q13421; Q13421; |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >8CXC_H|Chain B[auth H]|3F2 Antibody heavy chain|Mus musculus (10090) EEVQLLESGGGLVQPGGSLRLSCAASGLTFRSYAMTWVRQAPGKGLEWVSGISVSGGITYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKRGAAVGSFDYWGQGTLVTVSSAKTTAPSVYPLAPVTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRG |
Light Chain: L
Mutation: NULL
| >8CXC_L|Chain A[auth L]|3F2 Antibody light chain|Mus musculus (10090) DIQMTQSPSSLSASVGDRVTITCRSSQGIGSWLAWYQQKPEKAPQSLIYAASSLQSGVPSRFSGSGSGTDFTLTISNLQPEDFATYYCQQYNSYPLTFGGGTKVEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE |
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)
| L: GLY30 SER31 TRP32 TYR49 ALA50 ALA51 SER52 SER53 TYR91 H: SER31 TYR32 ALA33 VAL53 GLY100 ALA101 ALA102 VAL103 GLY104 SER105 M: SER525 GLN548 GLY552 PRO553 HIS554 VAL555 GLU556 GLY557 LYS559 ASP580 THR581 LEU582 GLY583 LEU584 GLY585 GLN587 |
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)
