Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1210 |
| PDBID: | 5BOZ |
| Chains: | J_D |
| Organism: | Ricinus communis, Vicugna pacos |
| Method: | XRD |
| Resolution (Å): | 3.10 |
| Reference: | 10.1074/jbc.M116.758102 |
| Antibody | |
| Antibody: | E1 VHH |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Ricin |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: J
Mutation: NULL
| >5BOZ_J|Chain B[auth G], D[auth H], F[auth I], H[auth J], J[auth K], L|VHH single chain antibody E1|Vicugna pacos (30538) NMQVQLVESGGGLVQAGGSLRLSCAASGRTFSRSSMGWFRQAPGKEREFVASIVWADGTTLYGDSVKGRFTVSRDNVKNMVYLQMNNLKPEDTALYYCADNKFVRGLVAVRAIDYDYWGQGTQVTVS |
Antigen
Chain: D
Mutation: NULL
| >5BOZ_D|Chain A, C[auth B], E[auth C], G[auth D], I[auth E], K[auth F]|Ricin|Ricinus communis (3988) KQYPIINFTTAGATVQSYTNFIRAVRGRLTTGADVRHEIPVLPNRVGLPINQRFILVELSNHAELSVTLALDVTNAYVVGYRAGNSAYFFHPDNQEDAEAITHLFTDVQNRYTFAFGGNYDRLEQLAGNLRENIELGNGPLEEAISALYYYSTGGTQLPTLARSFIICIQMISEAARFQYIEGEMRTRIRYNRRSAPDPSVITLENSWGRLSTAIQESNQGAFASPIQLQRRNGSKFSVYDVSILIPIIALMVYRCAPPPS |
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: THR28 PHE29 SER30 ARG31 SER32 ALA54 LYS100 PHE101 VAL102 ARG103 VAL106 ARG109 ALA110 ILE111 ASP112 TYR113 ASP114 TYR115 TRP116 D: HIS65 ALA66 ALA130 GLY131 ASN132 GLU135 ASN136 ILE137 GLU138 GLY142 PRO143 GLU145 GLU146 ALA147 SER149 ALA150 TYR153 GLY158 THR159 GLN160 PRO162 THR163 ARG166 SER167 ILE170 ARG197 SER198 ALA199 |
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)
