Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 3096 |
| PDBID: | 6W9G |
| Chains: | KM_B |
| Organism: | Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 1.82 |
| Reference: | 10.1021/acs.biochem.0c00474 |
| Antibody | |
| Antibody: | 5c8 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | CD40 ligand |
| Antigen mutation: | No |
| Durg Target: | P29965 |
Sequence information
Antibody
Heavy Chain: K
Mutation: NULL
| >6W9G_K|Chain D[auth H], F[auth K], H[auth X]|5c8* Fab (heavy chain)|Homo sapiens (9606) QVQLVQSGAEVVKPGASVKLSCKASGYIFTSYYMYWVKQAPGQGLEWIGEINPSNGDTNFNEKFKSKATLTVDKSASTAYMELSSLRSEDTAVYYCTRSDGRNDMDSWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT |
Light Chain: M
Mutation: NULL
| >6W9G_M|Chain E[auth L], G[auth M], I[auth Y]|5c8* Fab (light chain)|Homo sapiens (9606) DIVLTQSPATLSVSPGERATISCRASQRVSSSTYSYMHWYQQKPGQPPKLLIKYASNLESGVPARFSGSGSGTDFTLTISSVEPEDFATYYCQHSWEXPPTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: B
Mutation: NULL
| >6W9G_B|Chain A, B, C|CD40 ligand|Homo sapiens (9606) GDQNPQIAAHVISEASSKTTSVLQWAEKGYYTMSNNLVTLENGKQLTVKRQGLYYIYAQVTFCSNREASSQAPFIASLCLKSPGRFERILLRAANTHSSAKPCGQQSIHLGGVFELQPGASVFVNVTDPSQVSHGTGFTSFGLLKL |
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)
| K: THR30 SER31 TYR32 TYR33 ASN52 SER54 ASN55 GLY56 ASP57 ASN59 ASP100 GLY101 ARG102 ASN103 M: ARG28 SER30 SER31 SER32 THR33 TYR34 TYR36 SER95 TRP96 GLU97 B: SER128 GLU129 ALA130 SER131 SER132 ALA141 GLU142 LYS143 GLY144 TYR146 MET148 LEU155 ASN157 GLY158 CYS178 SER179 PRO217 CYS218 GLN220 SER245 GLN246 VAL247 SER248 HIS249 GLY250 THR251 PHE253 |
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)
