Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 806 |
| PDBID: | 4LGP |
| Chains: | B_A |
| Organism: | Ricinus communis, Vicugna pacos |
| Method: | XRD |
| Resolution (Å): | 2.40 |
| Reference: | 10.1016/j.jmb.2014.05.026 |
| Antibody | |
| Antibody: | VHH1 Nanobody |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Ricin |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: B
Mutation: NULL
| >4LGP_B|Chain B, D|VHH1 camelid nanobody|Vicugna pacos (30538) QVQLVETGGGLVQPGGSLTLSCAGSGGTLEHYAIGWFRQAPGKEHEWLVCNRGEYGSTVYVDSVKGRFTASRDNAKNTVYLQLNSLKPDDTGIYYCVSGCYSWRGPWGQGTQVTVS |
Antigen
Chain: A
Mutation: NULL
| >4LGP_A|Chain A, C|Ricin|Ricinus communis (3988) IFPKQYPIINFTTAGATVQSYTNFIRAVRGRLTTGADVRHEIPVLPNRVGLPINQRFILVELSNHAELSVTLALDVTNAYVVGYRAGNSAYFFHPDNQEDAEAITHLFTDVQNRYTFAFGGNYDRLEQLAGNLRENIELGNGPLEEAISALYYYSTGGTQLPTLARSFIICIQMISEAARFQYIEGEMRTRIRYNRRSAPDPSVITLENSWGRLSTAIQESNQGAFASPIQLQRRNGSKFSVYDVSILIPIIALMVYRCAP |
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: GLN1 VAL2 GLN3 GLU30 HIS31 TYR32 ALA33 TRP47 CYS50 ARG52 GLY53 TYR55 GLY56 SER98 GLY99 CYS100 TYR101 SER102 TRP103 ARG104 GLY105 PRO106 A: TYR91 HIS94 PRO95 ASN97 GLN98 ALA101 GLU102 THR105 HIS106 THR109 VAL111 GLN112 ASN113 ARG114 TYR115 THR116 PHE117 ALA118 PHE119 GLY120 ARG125 LEU129 TYR154 SER155 LEU161 |
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)
