Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1458 |
| PDBID: | 5JA9 |
| Chains: | B_D |
| Organism: | Vibrio cholerae O1 biovar El Tor str. N16961, Lama glama |
| Method: | XRD |
| Resolution (Å): | 1.85 |
| Reference: | 10.1093/nar/gkx138 |
| Antibody | |
| Antibody: | Nb6 Nanobody |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Toxin HigB-2 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: B
Mutation: NULL
| >5JA9_B|Chain C[auth A], D[auth B]|Nanobody 6|Lama glama (9844) QVQLQESGGGLVQPGGSLRLSCAASGFTFSNYAMRWYRQAPGEEREFVAFISSVGGSTNYADSVKGRFTISRDNGKNTLYLQMNSLKPEDTAVYFCVARLSLISDSWGQGTQVTVSSHHHHHH |
Antigen
Chain: D
Mutation: NULL
| >5JA9_D|Chain A[auth C], B[auth D]|Toxin HigB-2|Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (243277) MKSVFVESTIFEKYRDEYLSDEEYRLFQAELMLNPKLGDVIQGTGGLRKIRVASKGKGKRGGSRIIYYFLDEKRRFYLLTIYGKNEMSDLNANQRKQLMAFMEAWRNEQS |
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: TYR33 ALA34 ARG36 TYR38 GLU45 ARG46 PHE48 PHE51 ASN60 VAL98 ARG100 LEU101 SER102 LEU103 ILE104 SER105 ASP106 TRP108 D: ILE10 GLU12 LYS13 TYR14 ASP16 GLU17 TYR18 ILE66 LEU79 THR80 ILE81 TYR82 GLU86 MET87 LEU90 GLN94 GLN97 LEU98 PHE101 |
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)
