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Entry information

Complex
AACDB_ID: 5941
PDBID: 8CZ8
Chains: B_M
Organism: Homo sapiens
Method: XRD
Resolution (Å): 2.60
Reference: 10.3389/fddsv.2023.1216516
Antibody
Antibody: 1A12 scFv
Antibody mutation: No
INN (Clinical Trial):
Antigen
Antigen: Human mesothelin
Antigen mutation: No
Durg Target: Q13421; Q13421;

Sequence information

Antibody

Chain: B
Mutation: NULL

>8CZ8_B|Chain D[auth B], F[auth D]|scFv of A12 anti-mesothelin antibody|Homo sapiens (9606)
DIQMTQSPSSLSASVGDRVTITCRSSQGIGSWLAWYQQKPEKAPQSLIYAASSLQSGVPSRFSGSGSGTDFTLTISNLQPEDFATYYCQQYNSYPLTFGGGTKVEIKGGGSGGGSGGGSGGGSEVQLLESGGGLVQPGGSLRLSCAASGLTFRSYAMTWVRQAPGKGLEWVSGISVSGGITYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKRGAAVGSFDYWGQGTLVTVSS

Antigen

Chain: M
Mutation: NULL

>8CZ8_M|Chain B[auth E], C[auth M]|Mesothelin, cleaved form|Homo sapiens (9606)
GSDKDTLDTLTAFYPGYLCSLSPEELSSVPPSSIWAVRPQDLDTCDPRQLDVLYPKARLAFQNMNGSEYFVKIQSFLGGAPTEDLKALSQQNVSMDLATFMKLRTDAVLPLTVAEVQKLLGPHVEGLKAEERHRPVRDWILRQRQDDLDTLGLGLQGGI

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)

B: GLY30 SER31 TRP32 TYR49 ALA50 SER52 SER53 GLN55 TYR91 THR151 ARG153 SER154 TYR155 ALA156 VAL176 GLY223 ALA224 ALA225 VAL226 GLY227 SER228

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)

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