Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1454 |
| PDBID: | 5JA8 |
| Chains: | D_C |
| Organism: | Vibrio cholerae O1 biovar El Tor str. N16961, Lama glama |
| Method: | XRD |
| Resolution (Å): | 2.49 |
| Reference: | 10.1093/nar/gkx138 |
| Antibody | |
| Antibody: | Nb2 Nanobody |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Toxin HigB-2 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: D
Mutation: NULL
| >5JA8_D|Chain B, D, F, H|Nanobody 2|Lama glama (9844) QVQLQESGGGLVQPGGSLRLSCAASGFTLDYYAIGWFRQAPGKEREGVSCISSSGGTTNYADSVKGRFTVSRDNAKNTVYLQMNSLKPEDTAVYYCVADFACPLIREYDYWGQGTQVTVSSHHHHHH |
Antigen
Chain: C
Mutation: NULL
| >5JA8_C|Chain A, C, E, G|Toxin HigB-2|Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (243277) HMKSVFVESTIFEKYRDEYLSDEEYRLFQAELMLNPKLGDVIQGTGGLRKIRVASKGKGKRGGSRIIYYFLDEKRRFYLLTIYGKNEMSDLNANQRKQLMAFMEAWRNEQS |
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: GLN2 VAL3 PHE28 THR29 TYR32 TYR33 SER53 SER54 THR58 ALA99 ASP100 PHE101 ALA102 CYS103 PRO104 LEU105 ILE106 ARG107 GLU108 ASP110 TYR111 TRP112 C: SER8 THR9 ILE10 GLU12 LYS13 TYR14 TYR18 LEU79 THR80 ILE81 TYR82 ASN85 GLU86 MET87 SER88 LEU90 ASN91 ASN93 GLN94 GLN97 LEU98 PHE101 ALA104 TRP105 GLU108 |
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)
