Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 7088 |
| PDBID: | 5D1Q |
| Chains: | BA_E |
| Organism: | Homo sapiens, Staphylococcus aureus RF122 |
| Method: | XRD |
| Resolution (Å): | 3.22 |
| Reference: | 10.1038/ncomms13376 |
| Antibody | |
| Antibody: | D2-06-N2 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Iron-regulated surface determinant protein B (IsdB) NEAT2 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: B
Mutation: NULL
| >5D1Q_B|Chain B|D2-06 Heavy Chain|Homo sapiens (9606) QVQLVQSGAEVKKPASSVKVSCQASGGSFSTRTISWLRQAPGQGLEWMGGISPIFGAANYAQRFQGRVTITADKSTSTAYMELTSLTSEDTAVYYCARDRPPGAQFDTWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCGGGSGHHHHHHHHHHGGDYKDHDGDYKDHDIDYKDDDDK |
Light Chain: A
Mutation: NULL
| >5D1Q_A|Chain A|D2-06 Light Chain|Homo sapiens (9606) DIQLTQSPSSVSASVGDRITITCRASQDISNWVAWYQQKPGKAPKLLIYSASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQANTFPWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: E
Mutation: NULL
| >5D1Q_E|Chain E|Iron-regulated surface determinant protein B|Staphylococcus aureus (strain bovine RF122 / ET3-1) (273036) PGKMTDLQDTKYVVYESVENNESMMDTFVKHPIKTGMLNGKKYMVMETTNDDYWKDFMVEGQRVRTISKDAKNNTRTIIFPYVEGKTLYDAIVKVHVKTIDYDGQYHVRIVDKEAFTKAN |
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)
| Chain residues position delta_SASA
: residuesposition A: TRP32 ALA91 ASN92 PHE94 TRP96 B: SER30 THR31 ARG32 THR33 SER35 TRP47 GLY50 ILE51 ILE53 PHE54 GLY55 ALA56 ALA57 ASN58 ASP95 PRO97 PRO98 GLY99 PHE100 E: MET362 MET363 THR365 PHE366 ASN388 ASP390 TYR391 ASN412 VAL433 VAL435 LYS436 THR437 ILE438 ASP439 TYR440 TYR444 |
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)
