Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1851 |
| PDBID: | 5VXK |
| Chains: | B_A |
| Organism: | Vicugna pacos, Shigella flexneri |
| Method: | XRD |
| Resolution (Å): | 2.55 |
| Reference: | Not available or To be published |
| Antibody | |
| Antibody: | JMK-H2 VH-sdAb |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Invasin IpaD |
| Antigen mutation: | Yes |
| Durg Target: | |
Sequence information
Antibody
Chain: B
Mutation: NULL
| >5VXK_B|Chain A[auth B]|single-domain antibody JMK-H2|Vicugna pacos (30538) GSTQLQLVESGGGLVQPGGSLRLSCAASGFTLDDQPIAWFRQAPGKEREGVSCISIDGNTQSYSDSVKGRFTISRDTANNRVHLQMNNLKPEDTAVYYCAADRYTSVRQMCTMIEGLHRVWGQGTQVTVSSEPKTPKPQPRQGAPVPYPDPLEPR |
Antigen
Chain: A
Mutation: C289S
| >5VXK_A|Chain B[auth A]|Invasin IpaD|Shigella flexneri (623) GSTGSHPVSSLTMLNDTLHNIRTTNQALKKELSQKTLTKTSLEEIALHSSQISMDVNKSAQLLDILSRNEYPINKDARELLHSAPKEAELDGDQMISHRELWAKIANSINDINEQYLKVYEHAVSSYTQMYQDFSAVLSSLAGWISPGGNDGNSVKLQVNSLKKALEELKEKYKDKPLYPANNTVSQEQANKWLTELGGTIGKVSQKNGGYVVSINMTPIDNMLKSLDNLGGNGEVVLDNAKYQAWNAGFSAEDETMKNNLQTLVQKYSNANSIFDNLVKVLSSTISSS |
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: THR57 SER59 ARG100 TYR101 THR102 SER103 VAL104 ARG105 GLN106 MET107 CYS108 THR109 ILE111 GLY113 LEU114 ARG116 A: LYS68 TYR164 SER168 LEU171 SER172 LEU174 ALA175 ILE178 SER179 PRO180 GLY185 ASN186 SER187 VAL188 ASN273 ALA274 TYR276 GLN277 ASN280 ALA281 PHE283 SER284 ASP287 GLU288 LYS291 |
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)
