Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 7480 |
| PDBID: | 6OBE |
| Chains: | B_A |
| Organism: | Ricinus communis, Vicugna pacos |
| Method: | XRD |
| Resolution (Å): | 1.73 |
| Reference: | 10.1016/j.jmb.2020.01.006 |
| Antibody | |
| Antibody: | V6H8 VHH |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Ricin A chain |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: B
Mutation: NULL
| >6OBE_B|Chain B|VHH antibody V6H8|Vicugna pacos (30538) AQLQLVETGGGLVQAGGSLRLSCAASGSIFSMHAMGWFRQAPGRERELVAVAPTGRPSDYADFAKGRFTISRDNAKNTVSLQMHSLEPEDTAVYYCNAQLWERYVLNDYWGQGTQVTV |
Antigen
Chain: A
Mutation: NULL
| >6OBE_A|Chain A|Ricin A chain|Ricinus communis (3988) PKQYPIINFTTAGATVQSYTNFIRAVRGRLTTGADVRHEIPVLPNRVGLPINQRFILVELSNHAELSVTLALDVTNAYVVGYRAGNSAYFFHPDNQEDAEAITHLFTDVQNRYTFAFGGNYDRLEQLAGNLRENIELGNGPLEEAISALYYYSTGGTQLPTLARSFIICIQMISEAARFQYIEGEMRTRIRYNRRSAPDPSVITLENSWGRLSTAIQESNQGAFASPIQLQRRNGSKFSVYDVSILIPIIALMVYRCAPPPSSQF |
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: PHE29 SER30 MET31 HIS32 GLU44 ARG45 LEU47 THR53 GLY54 ARG55 ASP58 TYR59 ALA60 GLN98 TRP100 GLU101 ARG102 TYR103 VAL104 LEU105 ASN106 ASP107 A: ARG48 ASN78 TYR80 VAL82 PHE93 HIS94 PRO95 ASP96 ASN97 GLU99 ASP100 GLY121 ASN122 TYR123 ASP124 ARG125 GLU127 GLN128 LEU133 ARG134 GLU135 ARG180 ILE205 GLU208 ASN209 TRP211 GLY212 ARG213 SER228 PRO229 GLN231 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)
