Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 458 |
| PDBID: | 3DVN |
| Chains: | BA_Y |
| 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: | Yes |
| Durg Target: | Q8ID50; P0CG47; P0CG47; P0CG47; P0CG48; P0CG48; P0CG48; P0CG48; P0CG48; P0CG48; P0CG48; P0CG48; P0CG48; |
Sequence information
Antibody
Heavy Chain: B
Mutation: NULL
| >3DVN_B|Chain B, F[auth H]|Human IgG1 fab fragment heavy chain|Homo sapiens (9606) EISEVQLVESGGGLVQPGGSLRLSCAASGFNVKTGLIHWVRQAPGKGLEWVAYISPYYGSTSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCAREYYRWYTAIDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH |
Light Chain: A
Mutation: NULL
| >3DVN_A|Chain A, E[auth L]|Human IgG1 fab fragment light chain|Homo sapiens (9606) SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQYSSYSSLFTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: Y
Mutation: K66R
| >3DVN_Y|Chain D[auth V], H[auth Y]|Ubiquitin|Homo sapiens (9606) GSHMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQRESTLHLVLRLRGG |
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)
| A: ALA32 TYR91 SER96 PHE98 B: ASN28 LYS30 THR31 GLY32 LEU33 TYR50 SER52 TYR54 TYR55 GLU99 TYR100 TYR101 TYR104 THR105 Y: THR7 LEU8 THR9 GLU34 GLY35 ILE36 PRO37 ASP39 GLN40 LEU69 LEU71 ARG72 LEU73 ARG74 GLY75 GLY76 |
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)
