Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5030 |
| PDBID: | 7TGF |
| Chains: | B_A |
| Organism: | Ricinus communis, Vicugna pacos |
| Method: | XRD |
| Resolution (Å): | 1.35 |
| Reference: | 10.1016/j.jbc.2022.101742 |
| Antibody | |
| Antibody: | V9B2 VHH |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Ricinus communis ricin chain A |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: B
Mutation: NULL
| >7TGF_B|Chain B|VHH camelid antibody|Vicugna pacos (30538) QVQLAETGGGLVQPGGSLRLSCAASGFTLDDYAIGWFRQAPGKEREGVSCISSSDGRTYYADSVKGRFTISRDNAKNTVYLQMNSLKSEDTAVYYCATEEVCTLGIFGHGPDDYWGQGTQVTVSSEPKTPKPQ |
Antigen
Chain: A
Mutation: NULL
| >7TGF_A|Chain A|Ricin chain A|Ricinus communis (3988) IFPKQYPIINFTTAGATVQSYTNFIRAVRGRLTTGADVRHEIPVLPNRVGLPINQRFILVELSNHAELSVTLALDVTNAYVVGYRAGNSAYFFHPDNQEDAEAITHLFTDVQNRYTFAFGGNYDRLEQLAGNLRENIELGNGPLEEAISALYYYSTGGTQLPTLARSFIICIQMISEAARFQYIEGEMRTRIRYNRRSAPDPSVITLENSWGRLSTAIQESNQGAFASPIQLQRRNGSKFSVYDVSILIPIIALMVYRCAPPPSSQF |
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: ASP31 TYR32 SER52 SER53 SER54 ASP55 ARG57 TYR59 TYR60 ASP62 LYS65 GLU100 VAL101 CYS102 THR103 LEU104 ILE106 PHE107 GLY108 HIS109 GLY110 PRO111 ASP112 ASP113 A: GLN19 THR22 ARG26 GLU41 GLN182 TYR183 GLY186 ARG189 THR190 ARG193 TYR194 ARG196 SER203 LEU207 LEU232 GLN233 ARG234 ARG235 PHE240 ASP244 SER246 ILE247 LEU248 ILE249 PRO250 ILE251 |
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)
