Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1770 |
| PDBID: | 5UMI |
| Chains: | HL_C |
| Organism: | Clostridioides difficile, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 3.23 |
| Reference: | 10.1074/jbc.M117.781112 |
| Antibody | |
| Antibody: | PA50 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Toxin A |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >5UMI_H|Chain C[auth A], E[auth H]|PA50 Fab Heavy chain|Homo sapiens (9606) QVQLVQSGAEVKKPGASVKVSCKASGYTFTDYNMDWVRQAPGQRLEWMGDINPKYDIIGHNPKFMGRVTITRDTSASTAYMELSSLRSEDTAVYYCARSDRGWYFDVWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC |
Light Chain: L
Mutation: NULL
| >5UMI_L|Chain B, D[auth L]|PA50 Fab Light chain|Homo sapiens (9606) EIVLTQSPATLSLSPGERATLSCRASSSVNYMNWYQQKPGQAPRPLIYATSNLASGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQWSSRTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: C
Mutation: NULL
| >5UMI_C|Chain A[auth C]|Toxin A|Clostridioides difficile (1496) MGSSHHHHHHSSGLVPRGSHMGLRTIDGKKYYFNTNTAVAVTGWQTINGKKYYFNTNTSIASTGYTIISGKHFYFNTDGIMQIGVFKGPDGFEYFAPANTDANNIEGQAIRYQNRFLYLHDNIYYFGNNSKAATGWVTIDGNRYYFEPNTAMGANGYKTIDNKNFYFRNGLPQIGVFKGSNGFEYFAPANTDANNIEGQAIRYQNRFLHLLGKIYYFGNNSKAVTGWQTINGKVYYFMPDTAMAAAGGLFEIDGVIYFFGVDGVKAPGIYG |
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: GLU1 ILE2 ASN30 TYR31 GLN89 TRP90 SER91 SER92 ARG93 H: ASP31 TYR32 ASN33 TRP47 ASP50 ASN52 LYS54 TYR55 ASP56 ILE57 ILE58 GLY59 HIS60 ASN61 PRO62 LYS63 MET65 SER99 ARG101 GLY102 TRP103 C: ILE2522 TYR2533 PRO2536 ASN2538 THR2539 ASP2540 ALA2541 ASN2542 GLU2545 ARG2550 TYR2551 GLN2552 ASN2553 ARG2554 PHE2555 LEU2556 TYR2557 LEU2558 HIS2559 ASP2560 ILE2562 TYR2564 ASN2567 ILE2578 ASP2579 TYR2583 LEU2610 |
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)
