Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 7156 |
| PDBID: | 5M2M |
| Chains: | D_B |
| Organism: | Homo sapiens, Lama glama |
| Method: | XRD |
| Resolution (Å): | 2.30 |
| Reference: | 10.3389/fimmu.2017.00867 |
| Antibody | |
| Antibody: | 3 VHH |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Tumor necrosis factor (TNF) |
| Antigen mutation: | No |
| Durg Target: | P01375 |
Sequence information
Antibody
Chain: D
Mutation: NULL
| >5M2M_D|Chain D, E, F, H, J, L[auth N]|Llama nanobody VHH3|Lama glama (9844) QVQLQESGGGLVQPGGSLRLSCAASGRTFSDHSGYTYTIGWFRQAPGKEREFVARIYWSSGNTYYADSVKGRFAISRDIAKNTVDLTMNNLEPEDTAVYYCAARDGIPTSRSVESYNYWGQGTQVTVSS |
Antigen
Chain: B
Mutation: NULL
| >5M2M_B|Chain A, B, C, G, I, K[auth M]|Tumor necrosis factor|Homo sapiens (9606) VRSSSRTPSDKPVAHVVANPQAEGQLQWLNRRANALLANGVELRDNQLVVPSEGLYLIYSQVLFKGQGCPSTHVLLTHTISRIAVSYQTKVNLLSAIKSPCQRETPEGAEAKPWYEPIYLGGVFQLEKGDRLSAEINRPDYLDFAESGQVYFGIIAL |
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: HIS32 TYR35 THR36 ARG55 TYR57 SER59 SER60 GLY61 ASN62 TYR64 ASP67 LYS70 ARG77 ILE79 ALA80 ILE107 PRO108 THR109 SER110 ARG111 TYR116 B: PRO20 GLN21 ALA22 GLU23 GLY24 GLN25 LYS65 GLY66 GLN67 CYS69 PRO70 THR72 GLU104 THR105 GLU107 GLY108 ALA111 ASN137 ARG138 PRO139 ASP140 TYR141 LEU142 PHE144 ALA145 GLU146 |
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)
