Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1266 |
| PDBID: | 5DMJ |
| Chains: | E_D |
| Organism: | Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 2.79 |
| Reference: | 10.1016/j.jmb.2016.05.014 |
| Antibody | |
| Antibody: | 3H56-5 VH-sdAb |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Tumor necrosis factor receptor superfamily member 5(extracellular domain of the CD40) |
| Antigen mutation: | No |
| Durg Target: | P25942 |
Sequence information
Antibody
Chain: E
Mutation: NULL
| >5DMJ_E|Chain B, D[auth E], F[auth G]|3H65-5 domain antibody (dAb)|Homo sapiens (9606) STEVQLLESGGGLVQPGGSLRLSCAASGFTFRDYEMWWVRQAPGKGLERVSAINPQGTRTYYADSVMGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKLPFTFDDWGQGTLVTVSSAAA |
Antigen
Chain: D
Mutation: NULL
| >5DMJ_D|Chain A, C[auth D], E[auth F]|Tumor necrosis factor receptor superfamily member 5|Homo sapiens (9606) PTACREKQYLINSQCCSLCQPGQKLVSDCTEFTETECLPCGESEFLDTWNRETHCHQHKYCDPNLGLRVQQKGTSETDTICTCEEGWHCTSEACESCVLHRSCSPGFGVKQIATGVSDTICEPCPVGFFSDVSSAFEKCHPWTSCETKDLVVQQAGTDKTDVVCGPQDRLRDPGGGGGRLVPR |
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)
| E: GLU33 TRP35 VAL37 GLN39 GLY44 LEU45 ARG47 ALA50 ILE51 PRO52 ARG56 THR57 TYR58 ALA93 LEU95 PRO96 PHE97 THR98 PHE99 ASP101 TRP103 D: PRO85 ASN86 LEU87 GLY88 GLU107 GLY108 TRP109 HIS110 CYS119 VAL120 LEU121 HIS122 SER124 GLN133 ILE134 THR136 VAL154 SER155 SER156 ALA157 PHE158 GLU159 LYS160 HIS162 |
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)
