Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6336 |
| PDBID: | 8H3X |
| Chains: | A_C |
| Organism: | Bacteroides fragilis, Vicugna pacos |
| Method: | XRD |
| Resolution (Å): | 1.66 |
| Reference: | 10.3389/fimmu.2023.1065274 |
| Antibody | |
| Antibody: | 282 VHH |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Bacteroide fragilis toxin |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: A
Mutation: NULL
| >8H3X_A|Chain B[auth A]|nanobody 282|Vicugna pacos (30538) QVQLQESGGGLVQPGGSLRLSCAASGFTFSRYTMTWVRQAPGKGLEWVSNINSDGGRTYYADSVKGRFTISRDNTKNTLYLQMNSLKPEDTAVYYCAIPKRTYVPPSQFDDRGQGTQVTVSSHHHHHH |
Antigen
Chain: C
Mutation: NULL
| >8H3X_C|Chain A[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)
| A: THR28 ARG31 TYR32 THR33 ASN52 SER53 ASP54 ARG57 ILE98 PRO99 LYS100 ARG101 THR102 TYR103 ASP110 C: SER44 THR46 ASN87 ASP107 GLU108 TYR126 LYS127 GLU128 ALA129 GLN130 MET131 MET132 ASN133 GLU134 GLU137 ASP160 ARG162 ASP169 ILE170 VAL171 THR231 TYR233 |
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)
