Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1771 |
| PDBID: | 5UMI |
| Chains: | AB_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: A
Mutation: NULL
| >5UMI_A|Chain C[auth A], E[auth H]|PA50 Fab Heavy chain|Homo sapiens (9606) QVQLVQSGAEVKKPGASVKVSCKASGYTFTDYNMDWVRQAPGQRLEWMGDINPKYDIIGHNPKFMGRVTITRDTSASTAYMELSSLRSEDTAVYYCARSDRGWYFDVWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC |
Light Chain: B
Mutation: NULL
| >5UMI_B|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)
| B: ILE2 SER27 VAL29 ASN30 TYR31 GLN89 TRP90 SER91 SER92 ARG93 A: ASP31 TYR32 ASN33 TRP47 ASN52 LYS54 TYR55 ASP56 ILE57 ILE58 GLY59 HIS60 ASN61 PRO62 LYS63 MET65 GLY66 SER99 ARG101 GLY102 TRP103 C: ILE2613 TYR2624 PRO2627 ASN2629 THR2630 ASP2631 ALA2632 ASN2633 GLU2636 ARG2641 TYR2642 GLN2643 ASN2644 ARG2645 PHE2646 LEU2647 HIS2648 LEU2649 LEU2650 ILE2653 TYR2655 ASN2658 ILE2669 ASN2670 LYS2672 TYR2674 ASP2701 |
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)
