Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1844 |
| PDBID: | 5VQM |
| Chains: | HL_A |
| Organism: | Clostridioides difficile R20291, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 2.79 |
| Reference: | 10.1074/jbc.M117.813428 |
| Antibody | |
| Antibody: | PA41 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Toxin B |
| Antigen mutation: | No |
| Durg Target: | P18177 |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >5VQM_H|Chain C[auth D], F[auth H]|PA41 FAB HEAVY CHAIN|Homo sapiens (9606) QVQLVQSGAEVKKPGASVKVSCKASGYPFTNYFMHWVRQAPGQRLEWIGRINPYNGATSYSLNFRDKATITLDKSASTAYMELSSLRSEDTAVYYCARSTITSPLLDFWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC |
Light Chain: L
Mutation: NULL
| >5VQM_L|Chain B[auth C], E[auth L]|PA41 FAB LIGHT CHAIN|Homo sapiens (9606) EIVLTQSPATLSLSPGERATLSCRASQSVGTSIHWYQQKPGQAPRLLIKFASESISGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQSNKWPFTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: A
Mutation: NULL
| >5VQM_A|Chain A, D[auth B]|Toxin B|Peptoclostridium difficile (645463) MSLVNRKQLEKMANVRFRVQEDEYVAILDALEEYHNMSENTVVEKYLKLKDINSLTDIYIDTYKKSGRNKALKKFKEYLVTEVLELKNNNLTPVEKNLHFVWIGGQINDTAINYINQWKDVNSDYNVNVFYDSNAFLINTLKKTIVESATNDTLESFRENLNDPRFDYNKFYRKRMEIIYDKQKNFINYYKTQREENPDLIIDDIVKIYLSNEYSKDIDELNSYIEESLNKVTENSGNDVRNFEEFKGGESFKLYEQELVERWNLAAASDILRISALKEVGGVYLDVDMLPGIQPDLFESIEKPSSVTVDFWEMVKLEAIMKYKEYIPGYTSEHFDMLDEEVQSSFESVLASKSDKSEIFSSLGDMEASPLEVKIAFNSKGIINQGLISVKDSYCSNLIVKQIENRYKILNNSLNPAISEDNDFNTTTNAFIDSIMAEANADNGRFMMELGKYLRVGFFPDVKTTINLSGPEAYAAAYQDLLMFKEGSMNIHLIEADLRNFEISKTNISQSTEQEMASLWSFDDARAKAQFEEYKKNYFEGSLGHAGLRGSHHHHHH |
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: SER28 GLY30 THR31 SER32 LYS49 PHE50 GLU53 SER67 GLY68 SER91 ASN92 LYS93 H: ASN31 TYR32 PHE33 ARG50 ASN52 TYR54 ASN55 ALA57 THR100 ILE101 THR102 SER103 LEU105 A: ASN116 GLN117 ASP120 LYS322 TYR323 LYS324 GLU325 TYR326 PRO328 GLU340 GLU341 GLN343 SER344 SER345 GLU347 SER348 LEU350 ALA351 SER352 LYS353 SER354 ASP355 |
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)
