Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6337 |
| PDBID: | 8H3Y |
| Chains: | D_B |
| Organism: | Bacteroides fragilis, Vicugna pacos |
| Method: | XRD |
| Resolution (Å): | 2.25 |
| Reference: | 10.3389/fimmu.2023.1065274 |
| Antibody | |
| Antibody: | 327 VHH |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Bacteroide fragilis toxin |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: D
Mutation: NULL
| >8H3Y_D|Chain C[auth D], D[auth E], E[auth F]|Nanobody 327|Vicugna pacos (30538) QVQLQESGGGLVQAGGSLRLSCTYSGQTFSAWAMGWFRQAPGKERETVATINWNGERTQYADAVKGRFTISRDNAKDTVYLEMNSLKPEDTAVYYCASMMGTYYSGSPKNWGQGTQVTVSSHHHHHH |
Antigen
Chain: B
Mutation: NULL
| >8H3Y_B|Chain A, B, F[auth C]|Fragilysin|Bacteroides fragilis (817) MKNVKLLLMLGTAALLAACSNEADSLTTSIDAPVTASIDLQSVSYTDLATQLNDVSDFGKMIILKDNGFNRQVHVSMDKRTKIQLDNENVRLFNGRDKDSTSFILGDEFAVLRFYRNGESISYIAYKEAQMMNEIAEFYAAPFKKTRAINEKEAFECIYDSRTRSAGKDIVSVKINIDKAKKILNLPECDYINDYIKTPQVPHGITESQTRAVPSEPKTVYVICLRENGSTIYPNEVSAQMQDAANSVYAVHGLKRYVNFHFVLYTTEYSCPSGDAKEGLEGFTASLKSNPKAEGYDDQIYFLIRWGTWDNKILGMSWFNSYNVNTASDFEASGMSTTQLMYPGVMAHELGHILGAEHTDNSKDLMYATFTGYLSHLSEKNMDIIAKNLGWEAADGD |
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: VAL2 TYR24 GLN27 THR28 SER30 ALA31 TRP32 ALA33 ASN52 TRP53 ARG57 MET100 GLY101 THR102 TYR103 TYR104 LYS109 ASN110 B: HIS252 HIS358 THR359 ASP360 ASN361 LYS363 LEU377 SER378 GLU379 LYS380 MET382 ASP383 LYS387 ALA393 ASP397 |
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)
