Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 7484 |
| PDBID: | 6OBO |
| Chains: | C_A |
| Organism: | Ricinus communis, Vicugna pacos |
| Method: | XRD |
| Resolution (Å): | 1.90 |
| Reference: | 10.1016/j.jmb.2020.01.006 |
| Antibody | |
| Antibody: | V6A6 VHH |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Ricin A chain |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: C
Mutation: NULL
| >6OBO_C|Chain C, D|VHH antibody V6A6|Vicugna pacos (30538) VQLAETGGGLAQAGGSLRLSCAASGSIFSINAMGWYRQAPGKERELVADISGSGRTNYADSVKGRFTISRDNAKNTVSLQMNSLKPEDTAVYYCNVVGGSYYYDEYNYWGQGTQVTVSSEP |
Antigen
Chain: A
Mutation: NULL
| >6OBO_A|Chain A, B|Ricin A chain|Ricinus communis (3988) QYPIINFTTAGATVQSYTNFIRAVRGRLTTGADVRHEIPVLPNRVGLPINQRFILVELSNHAELSVTLALDVTNAYVVGYRAGNSAYFFHPDNQEDAEAITHLFTDVQNRYTFAFGGNYDRLEQLAGNLRENIELGNGPLEEAISALYYYSTGGTQLPTLARSFIICIQMISEAARFQYIEGEMRTRIRYNRRSAPDPSVITLENSWGRLSTAIQESNQGAFASPIQLQRRNGSKFSVYDVSILIPIIALMVYRCAP |
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)
| C: PHE29 SER30 ILE31 ASN32 TYR37 GLU44 ARG45 GLU46 LEU47 SER52 GLY53 SER54 GLY55 ARG56 ASN58 ASP61 ASN73 ASN96 VAL98 GLY100 SER101 TYR102 TYR103 TYR104 ASP105 GLU106 TYR107 ASN108 A: ASP75 ASN78 TYR80 VAL82 PHE93 HIS94 PRO95 ASP96 ASP100 ILE104 ALA118 PHE119 GLY120 GLY121 ASN122 TYR123 ASP124 ARG125 GLU127 GLN128 LEU133 ARG134 GLU135 ARG180 ILE205 GLU208 ASN209 TRP211 GLY212 ARG213 ALA227 SER228 PRO229 ILE230 GLN231 GLN233 SER238 LYS239 TYR243 VAL256 ARG258 |
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)
