Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 7489 |
| PDBID: | 6OCD |
| Chains: | D_C |
| Organism: | Ricinus communis, Vicugna pacos |
| Method: | XRD |
| Resolution (Å): | 2.10 |
| Reference: | 10.1016/j.jmb.2020.01.006 |
| Antibody | |
| Antibody: | V6D4 VHH |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Ricin A chain |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: D
Mutation: NULL
| >6OCD_D|Chain B, D|VHH antibody V6D4|Vicugna pacos (30538) QLVETGGGLVQSGGSLRLSCAASGFTLDNYNIGWFRQAPGKEYGGVSCISSSDGSTYYADSVKGRFTISRDNAKNTVYLQMNNLKPEDTDVYYCAATKYGSSCPIRPYDYWGQGTQVTVSSAH |
Antigen
Chain: C
Mutation: NULL
| >6OCD_C|Chain A, C|Ricin A chain|Ricinus communis (3988) QYPIINFTTAGATVQSYTNFIRAVRGRLTTGADVRHEIPVLPNRVGLPINQRFILVELSNHAELSVTLALDVTNAYVVGYRAGNSAYFFHPDNQEDAEAITHLFTDVQNRYTFAFGGNYDRLEQLAGNLRENIELGNGPLEEAISALYYYSTGGTQLPTLARSFIICIQMISEAARFQYIEGEMRTRIRYNRRSAPDPSVITLENSWGRLSTAIQESNQGAFASPIQLQRRNGSKFSVYDVSILIPIIALMVYRCAPP |
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: TYR32 PHE37 GLN39 ALA40 PRO41 GLY42 GLU44 TYR45 GLY46 TYR59 THR99 LYS100 TYR101 GLY102 ILE107 ARG108 PRO109 TYR110 ASP111 TYR112 TRP113 GLY114 GLN115 C: ARG48 ASN78 TYR80 HIS94 PRO95 ASP96 ASN97 GLN98 ASP100 ALA101 ALA118 PHE119 GLY120 ASN122 ASP124 ARG125 GLN128 ASN209 TRP211 GLY212 ARG213 THR216 GLU220 VAL256 ARG258 CYS259 |
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)
