Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1852 |
| PDBID: | 5VXL |
| Chains: | B_A |
| Organism: | Shigella flexneri, Vicugna pacos |
| Method: | XRD |
| Resolution (Å): | 2.80 |
| Reference: | Not available or To be published |
| Antibody | |
| Antibody: | JPS-G3 VH-sdAb |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Invasin IpaD |
| Antigen mutation: | Yes |
| Durg Target: | |
Sequence information
Antibody
Chain: B
Mutation: NULL
| >5VXL_B|Chain B|single-domain antibody JPS-G3|Vicugna pacos (30538) GSTQVQLAESGGGLVQPGGSLRLSCSASGGVFIIYNMGWYRQAPGKQRELVASIDSYSGSITNYADSVKGRFTISRDNVEKRVYLEMNNLKPEDTAVYYCNANLRTNNYWGQGTQVTVSSEPKTPKPQPARQGAPVPYPDPLEP |
Antigen
Chain: A
Mutation: C289S
| >5VXL_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: GLY27 VAL28 ILE30 ILE31 ASP52 SER53 TYR54 SER55 SER57 ILE58 ASN75 VAL76 LYS78 LEU101 ARG102 A: LYS72 GLN162 GLN165 ASP166 ALA169 VAL170 SER172 SER173 ALA175 GLY176 TRP177 GLN191 SER194 LYS197 ALA198 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)
