Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 2304 |
| PDBID: | 6IBB |
| Chains: | D_C |
| Organism: | Rattus norvegicus, Vicugna pacos |
| Method: | XRD |
| Resolution (Å): | 2.12 |
| Reference: | 10.1038/s41586-019-1663-8 |
| Antibody | |
| Antibody: | 6 Nanobody |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Succinate receptor 1 SUCNR1 (GPR91) |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: D
Mutation: NULL
| >6IBB_D|Chain B, D|Nanobody6|Vicugna pacos (30538) DYKDDDDKEVQLVESGGGLVQPGGSLRLSCEASGYTLANYAIGWFRQAPGKEREGVSCISSGGSTVYSESVKDRFTISRDNAKKIVYLQMNSLQPEDTAVYYCAADPFGERLCIDPNTFAGYLETWGQGTQVTVSSLEVLFQ |
Antigen
Chain: C
Mutation: NULL
| >6IBB_C|Chain A, C|Succinate receptor 1|Rattus norvegicus (10116) DYKDDDDKAQNLSCENWLALENILKKYYLSAFYGIEFIVGMLGNFTVVFGYLFCMKNWNSSNVYLFNLSISDLAFLCTLPMLIRSYATGNWTYGDVLCISNRYVLHANLYTSILFLTFISIDRYLLMKFPFREHILQKKEFAILISLAVWVLVTLEVLPMLTFITSTPIEKGDSCVDYASSGNPKYSLIYSLCLTLLGFLIPLSVMCFFYYKMVVFLKKRSQQQATVLSLNKPLRLVVLAVVIFSVLFTPYHIMRNVRIASRLDSWPQGCSQKAIKCLYILTRPLAFLNSAVNPIFYFLVGDHFRDMLFSKLRQYFKSLTSFRLLEVLFQGPHHHHHHHHHH |
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: GLU54 GLY55 VAL56 SER57 VAL66 TYR67 SER68 GLU69 SER70 PHE108 GLU110 ARG111 CYS113 ILE114 ASP115 PRO116 ASN117 THR118 PHE119 GLY121 TYR122 C: MET48 LYS49 ASN50 ASN52 ASN55 ARG116 LEU119 PHE122 PRO123 PHE124 ARG125 GLU126 ARG213 LYS225 VAL293 GLY294 ASP295 HIS296 ASP299 MET300 |
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)
