Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6188 |
| PDBID: | 8FD0 |
| Chains: | C_A |
| Organism: | Bos taurus, Lama glama |
| Method: | XRD |
| Resolution (Å): | 3.71 |
| Reference: | 10.1038/s41467-023-40911-9 |
| Antibody | |
| Antibody: | Nb2 VHH |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Bos taurus rhodopsin |
| Antigen mutation: | No |
| Durg Target: | P08100 |
Sequence information
Antibody
Chain: C
Mutation: NULL
| >8FD0_C|Chain C, D|Nanobody Nb2|Lama glama (9844) QVQLVESGGGLVQPGGSLRLSCAASGFTFSKYAMNWVRQPPGKGLEWVSGIRPSGDNPTYADSVEGRFTIIRDNDKKMVYLQMTSLKTEDTAVYYCTRGYGTMTIEGQGTQVTVSSHHHHHHEPEA |
Antigen
Chain: A
Mutation: NULL
| >8FD0_A|Chain A, B|Rhodopsin|Bos taurus (9913) MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA |
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)
| C: VAL2 PHE27 THR28 LYS31 TYR32 ALA33 ASN35 TRP47 GLY50 ILE51 ARG52 THR59 TYR60 ALA61 ASP62 GLY99 TYR100 GLY101 THR102 MET103 A: MET1 ASN2 GLY3 THR4 GLU5 GLY6 PRO7 TYR10 ASN15 LYS16 TYR192 THR193 PRO194 GLU196 GLU197 GLU201 GLN279 GLY280 |
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)
