Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 7136 |
| PDBID: | 5J56 |
| Chains: | B_A |
| Organism: | Ricinus communis, Vicugna pacos |
| Method: | XRD |
| Resolution (Å): | 1.80 |
| Reference: | 10.1074/jbc.M116.758102 |
| Antibody | |
| Antibody: | V1C7 VHH |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Ricin toxin |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: B
Mutation: NULL
| >5J56_B|Chain B|VHH single chain antibody V1C7|Vicugna pacos (30538) AQVQLVESGGGLVQPGGSLRLSCVASEFSGFTLDYYAIGWFRQAPGKEREGLSSISSSSDGFTSYSDSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAARLGGWASFSPQEYDYWGQGTQVTVSS |
Antigen
Chain: A
Mutation: NULL
| >5J56_A|Chain A|Ricin|Ricinus communis (3988) MIFPKQYPIINFTTAGATVQSYTNFIRAVRGRLTTGADVRHEIPVLPNRVGLPINQRFILVELSNHAELSVTLALDVTNAYVVGYRAGNSAYFFHPDNQEDAEAITHLFTDVQNRYTFAFGGNYDRLEQLAGNLRENIELGNGPLEEAISALYYYSTGGTQLPTLARSFIICIQMISEAARFQYIEGEMRTRIRYNRRSAPDPSVITLENSWGRLSTAIQESNQGAFASPIQLQRRNGSKFSVYDVSILIPIIALMVYRCAPPPSSQF |
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)
| Chain residues position delta_SASA
: residuesposition B: PHE30 ASP33 TYR34 SER55 SER56 SER57 SER58 ASP59 PHE61 ARG103 LEU104 GLY105 GLY106 TRP107 SER111 GLN113 GLU114 ASP116 A: HIS65 ALA66 GLU67 LEU68 GLU138 ASN141 GLY142 GLU145 GLU146 SER149 ALA150 TYR153 GLY157 GLY158 THR159 GLN160 THR163 ASN195 ARG197 |
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)
