Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 455 |
| PDBID: | 3DVN |
| Chains: | HL_U |
| Organism: | Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 2.70 |
| Reference: | 10.1016/j.cell.2008.07.039 |
| Antibody | |
| Antibody: | Apu2.16 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Ubiquitin |
| Antigen mutation: | No |
| Durg Target: | Q8ID50; P0CG47; P0CG47; P0CG47; P0CG48; P0CG48; P0CG48; P0CG48; P0CG48; P0CG48; P0CG48; P0CG48; P0CG48; |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >3DVN_H|Chain B, F[auth H]|Human IgG1 fab fragment heavy chain|Homo sapiens (9606) EISEVQLVESGGGLVQPGGSLRLSCAASGFNVKTGLIHWVRQAPGKGLEWVAYISPYYGSTSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCAREYYRWYTAIDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH |
Light Chain: L
Mutation: NULL
| >3DVN_L|Chain A, E[auth L]|Human IgG1 fab fragment light chain|Homo sapiens (9606) SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQYSSYSSLFTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: U
Mutation: NULL
| >3DVN_U|Chain C[auth U], G[auth X]|Ubiquitin D77|Homo sapiens (9606) GSHMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGD |
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)
| L: VAL29 SER30 SER31 TYR49 SER50 ALA51 SER52 SER53 LEU54 ARG66 H: TYR101 ARG102 TYR104 U: SER-1 GLU18 PRO19 SER20 ASP21 THR55 SER57 ASP58 ASN60 ILE61 GLN62 |
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)
