Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 617 |
| PDBID: | 3PNW |
| Chains: | BA_C |
| Organism: | Homo sapiens, synthetic construct |
| Method: | XRD |
| Resolution (Å): | 2.05 |
| Reference: | 10.1016/j.jmb.2012.11.037 |
| Antibody | |
| Antibody: | anti-TDRD3 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Tudor domain-containing protein 3 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: B
Mutation: NULL
| >3PNW_B|Chain B, E, H, K, N, Q, T, W|FAB heavy chain|Homo sapiens (9606) EISEVQLVESGGGLVQPGGSLRLSCAASGFNLSSSYMHWVRQAPGKGLEWVASISSSYGSTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARTVRGSKKPYFSGWAMDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTGGSHHHHHH |
Light Chain: A
Mutation: NULL
| >3PNW_A|Chain A, D, G, J, M, P, S, V|FAB light chain|Homo Sapiens (9606) SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQHGPFYWLFTFGQGTKVEIKRTVAAPSVFIFPPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGECGGSDYKDDDDK |
Antigen
Chain: C
Mutation: NULL
| >3PNW_C|Chain C, F, I, L, O, R, U, X|Tudor domain-containing protein 3|Homo sapiens (9606) GPEKILESSIPMEYAKMWKPGDECFALYWEDNKFYRAEVEALHSSGMTAVVKFIDYGNYEEVLLSNIKPIQTEAWEE |
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: SER29 VAL30 SER31 SER32 ALA33 SER51 HIS92 GLY93 PRO94 PHE95 TYR96 TRP97 B: SER34 TYR36 SER57 TYR58 SER60 TYR62 ARG104 LYS108 PRO109 TYR110 PHE111 GLY113 TRP114 C: TYR566 TRP567 GLU568 GLU578 ALA579 LEU580 HIS581 SER582 THR586 ALA587 VAL588 LYS590 ILE592 ASP593 TYR594 GLY595 ASN596 TYR597 GLU598 GLU599 LEU601 |
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)
