Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1805 |
| PDBID: | 5VEB |
| Chains: | AB_X |
| Organism: | Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 2.34 |
| Reference: | 10.1158/2159-8290.CD-16-1414 |
| Antibody | |
| Antibody: | anti-CDH6 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Cadherin-6 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: A
Mutation: NULL
| >5VEB_A|Chain A|anti-CDH6 Fab heavy chain|Homo sapiens (9606) QVQLLESGGGLVQPGGSLRLSCAASGFTFSSHGMHWVRQAPGKGLEWVSVISGSGSNTGYADSVXGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARQWGSYAFDSWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTH |
Light Chain: B
Mutation: NULL
| >5VEB_B|Chain B, D[auth L]|anti-CDH6 Fab light chain|Homo sapiens (9606) DIQMTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPKLLIYAVSTLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSGTFPPTTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: X
Mutation: NULL
| >5VEB_X|Chain E[auth X], F[auth Y]|Cadherin-6|Homo sapiens (9606) EFYETFVCEKAKADQLIQTLHAVDKDDPYSGHQFSFSLAPEAASGSNFTIQDNKDNTAGILTRKNGYNRHEMSTYLLPVVISDNDYPVQSSTGTVTVRVCACDHHGNMQSCHAEALIHPLEVLFQ |
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: VAL2 PHE27 THR28 SER30 SER31 HIS32 GLY33 VAL50 SER52 GLY53 SER54 ASN57 THR58 GLY59 ARG98 GLN99 TRP100 GLY101 SER102 TYR103 ASP106 B: SER30 SER31 TYR32 TYR49 ALA50 VAL51 SER52 THR53 LEU54 GLN55 SER56 GLY57 VAL58 SER60 SER63 GLY64 SER65 GLY66 SER67 PHE94 PRO95 X: ASP503 SER519 GLY520 HIS521 GLN522 PHE523 SER524 PHE525 SER526 LEU527 PRO529 ALA532 SER533 GLY534 THR538 ILE539 GLN540 ASP541 ASN542 LYS543 LEU550 ARG552 VAL569 SER571 ASP572 ASN573 ASP574 TYR575 PRO576 VAL577 |
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)
