Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5962 |
| PDBID: | 8DCN |
| Chains: | DE_F |
| Organism: | Mus musculus, Clostridioides difficile |
| Method: | XRD |
| Resolution (Å): | 2.60 |
| Reference: | 10.1128/jb.00456-22 |
| Antibody | |
| Antibody: | BINTOXB/9 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Clostridioides difficile ADP-ribosylating binary toxin binding subunit CdtB |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: D
Mutation: NULL
| >8DCN_D|Chain A, D|BINTOXB/9 Fab heavy chain|Mus musculus (10090) QVQLQQSGAELARPGASVKMSCKASGYTFTSYTMHWVKQRPGQGLEWIGYINPSNDYTSYNQKFKDKATLTADKSSSTAYMQLSSLTSEDSAVYYCARCWGYDPYYFDYWGQGTTLTVSSASTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDCGKGLEVLFQ |
Light Chain: E
Mutation: NULL
| >8DCN_E|Chain B, E|BINTOXB/9 Fab light chain|Mus musculus (10090) DIVMSQSPSLLAVSAGEKVTMSCKSSQSLLNSRTRKNYLAWYQQKPGQSPKVLIYWASTRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCKQSYNLLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC |
Antigen
Chain: F
Mutation: NULL
| >8DCN_F|Chain C, F|ADP-ribosylating binary toxin binding subunit CdtB|Clostridioides difficile (1496) MKIPTDQEIMDAHKIYFADLNFNPSTGNTYINGMYFAPTQTNKEALDYIQKYRVEATLQYSGFKDIGTKDKEMRNYLGDPNQPKTNYVNLRSYFTGGENIMTYKKLRIYAITPDDRELLVLSVDHHHHHH |
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)
| D: THR28 THR30 SER31 TYR32 THR33 SER53 LYS73 TRP96 GLY97 TYR98 ASP99 E: THR28 TRP50 F: LEU810 TYR812 SER813 LYS816 ASP817 ILE818 GLY819 LYS821 ARG843 SER844 TYR845 PHE846 THR847 GLY848 GLY849 GLU850 |
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)
