Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1853 |
| PDBID: | 5VXM |
| Chains: | B_A |
| Organism: | Shigella flexneri, Vicugna pacos |
| Method: | XRD |
| Resolution (Å): | 2.05 |
| Reference: | Not available or To be published |
| Antibody | |
| Antibody: | 20ipaD VH-sdAb |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Invasin IpaD |
| Antigen mutation: | Yes |
| Durg Target: | |
Sequence information
Antibody
Chain: B
Mutation: NULL
| >5VXM_B|Chain B|Single-domain antibody 20ipaD|Vicugna pacos (30538) GSTQVQLVESGGGLVQAGGSLRLSCAVSGLEMQSHAIGWFRQAPGKEREGVSCINDDGSTTRYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYFCAAKSVWFCSVIRSHEFNSWGQGTQVTVSSAHHSEDPSARQGAPVPYPDPLEP |
Antigen
Chain: A
Mutation: C289S
| >5VXM_A|Chain 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: ASN52 ASP53 ASP54 SER56 THR57 ARG59 VAL101 TRP102 PHE103 CYS104 SER105 VAL106 ARG108 GLU111 A: ASP166 ALA169 VAL170 SER173 GLY176 TRP177 GLN191 ASN193 SER194 LYS197 ALA198 GLU200 GLU201 LEU202 GLU204 LYS205 LYS209 |
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)
