Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5863 |
| PDBID: | 8CAF |
| Chains: | DC_E |
| Organism: | Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 2.66 |
| Reference: | 10.1038/s41589-023-01392-5 |
| Antibody | |
| Antibody: | N8C_Fab3b synthetic-Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Active conformation of NEDD8-linked cullins CUL1 WHO domain (CUL1WHB) |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: D
Mutation: NULL
| >8CAF_D|Chain B, D|Fab Heavy Chain|Homo sapiens (9606) EVQLVESGGGLVQPGGSLRLSCAASGFNFSSSSIHWVRQAPGKGLEWVASISSSYGYTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARDPFGWAAHGVGLDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP |
Light Chain: C
Mutation: NULL
| >8CAF_C|Chain A, C|Fab Light Chain|Homo sapiens (9606) DIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQSSYSLITFGQGTKVEIKRTVAAPSVFIFPPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR |
Antigen
Chain: E
Mutation: NULL
| >8CAF_E|Chain E, H|Cullin-1|Homo sapiens (9606) TTHKNIEEDRKLLIQAAIVRIMKMRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYLA |
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: SER28 VAL29 SER30 SER31 ALA32 TYR49 SER50 SER52 SER53 ARG66 SER91 SER92 TYR93 D: SER54 TYR55 GLY56 TYR57 TYR59 PHE101 TRP103 ALA104 ALA105 HIS106 VAL108 E: ARG717 ILE718 LYS720 MET721 ARG722 LYS723 VAL724 LEU725 LYS726 GLN729 GLY732 GLU733 THR736 GLN737 SER739 SER740 |
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)
