Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1850 |
| PDBID: | 5VXJ |
| Chains: | J_I |
| Organism: | Shigella flexneri, Vicugna pacos |
| Method: | XRD |
| Resolution (Å): | 2.50 |
| Reference: | Not available or To be published |
| Antibody | |
| Antibody: | JMK-E3 VH-sdAb |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Invasin IpaD |
| Antigen mutation: | Yes |
| Durg Target: | |
Sequence information
Antibody
Chain: J
Mutation: NULL
| >5VXJ_J|Chain B, D, F, H, J|single-domain antibody JMK-E3|Vicugna pacos (30538) GSTQVQLAETGGGLAQPGGSLRLSCAASGFTFSRAVMNWYRQAPGKERELVARIYDAGGNGSIADPVKGRFTISRDNAKNTVHLQMNSLKPEDTAMYVCNAGIFDGNYRTYWGQGTQVTVSSEPKTPKPQPARQGAPVPYPDPLEP |
Antigen
Chain: I
Mutation: C289S
| >5VXJ_I|Chain A, C, E, G, I|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)
| J: GLN1 GLN3 GLU6 THR7 GLY8 GLY9 LEU11 ALA12 GLN13 GLY15 SER17 LEU18 ARG19 SER21 ALA23 ALA54 GLY55 GLY56 ASN57 THR69 ILE70 SER71 ARG72 ASP73 ALA75 LYS76 THR78 HIS80 GLN82 ASN84 SER85 GLN111 GLY112 THR113 I: MET87 ASN90 LYS91 ALA93 GLN94 ASP97 ILE98 ARG101 GLU122 ARG132 GLU133 ALA136 LYS137 ALA139 ASN140 ASN143 ASP144 GLU147 GLN148 ASN216 THR217 VAL218 SER219 GLU221 |
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)
