Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 7487 |
| PDBID: | 6OCA |
| Chains: | D_B |
| Organism: | Ricinus communis, Vicugna pacos |
| Method: | XRD |
| Resolution (Å): | 2.11 |
| Reference: | 10.1016/j.jmb.2020.01.006 |
| Antibody | |
| Antibody: | V2G10 VHH |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Ricin A chain |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: D
Mutation: NULL
| >6OCA_D|Chain B[auth C], D|VHH antibody V2G10|Vicugna pacos (30538) VQLVETGGGVVQAGGSLRLSCVASGRTFSVSGRTFSDHGLGWFRQAPGKEREFVGSISWSVDGDATYYTDLANSVKGRFTISGVNAKNTVYLQMNSLKPEDTAVYYCAAGLRGGTYARTIYEYDYWGQGTQVTVSLEP |
Antigen
Chain: B
Mutation: NULL
| >6OCA_B|Chain A, C[auth B]|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)
| D: VAL2 THR28 VAL31 SER32 GLY33 ARG34 SER37 ASP38 SER59 TRP60 SER61 VAL62 ASP63 ASP65 TYR69 THR70 LEU112 ARG113 GLY114 THR116 TYR117 ALA118 ARG119 THR120 TYR122 GLU123 ASP125 TYR126 B: ASP96 ASN97 ASN122 ASP124 GLU127 GLN128 LEU133 ARG134 GLU135 ILE205 ASN209 GLY212 ARG213 THR216 ALA217 GLU220 ALA227 SER228 PRO229 ILE230 GLN231 GLN233 LYS239 PHE240 SER241 TYR243 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)
