Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 7483 |
| PDBID: | 6OBM |
| Chains: | B_A |
| Organism: | Ricinus communis, Vicugna pacos |
| Method: | XRD |
| Resolution (Å): | 2.50 |
| Reference: | 10.1016/j.jmb.2020.01.006 |
| Antibody | |
| Antibody: | V6A7 VHH |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Ricin A chain |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: B
Mutation: NULL
| >6OBM_B|Chain B|VHH antibody V6A7|Vicugna pacos (30538) QVQLVETGGGGLVQAGGSLRLSCAASGSISSLNAMGWYRQAPGKERELVADISASGRTNYADSVKGRFTISRDNAKNTVSLQMNSLKPEDTAVYYCNAVGGTYYYDEYDYWGQGTQVTVS |
Antigen
Chain: A
Mutation: NULL
| >6OBM_A|Chain A|Ricin A chain|Ricinus communis (3988) QYPIINFTTAGATVQSYTNFIRAVRGRLTTGADVRHEIPVLPNRVGLPINQRFILVELSNHAELSVTLALDVTNAYVVGYRAGNSAYFFHPDNQEDAEAITHLFTDNQNRYTFAFGGNYDRLEQLAGNLRENIELGNGPLEEAISALYYYSTGGTQLPTLARSFIICIQMISEAARFQYIEGEMRTRIRYNRRSAPDPSVITLENSWGRLSTAIQESNQGAFASPIQLQRRNGSKFSVYDVSILIPIIALMVYRCAPPP |
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: SER30 SER31 LEU32 ASN33 TYR38 GLU45 ARG46 GLU47 LEU48 ASP51 SER53 ALA54 SER55 GLY56 ARG57 ASN59 TYR60 ALA61 ASP62 LYS65 ASN74 ASN97 VAL99 GLY101 THR102 TYR103 TYR104 TYR105 ASP106 GLU107 TYR108 ASP109 A: ASP75 ASN78 TYR80 VAL82 PHE93 HIS94 PRO95 ASP96 ASP100 ILE104 GLY120 GLY121 ASN122 TYR123 ASP124 ARG125 GLU127 GLN128 LEU133 ARG134 GLU135 ARG180 ILE205 GLU208 ASN209 TRP211 GLY212 ARG213 SER228 PRO229 GLN231 GLN233 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)
