Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 7090 |
| PDBID: | 5D1X |
| Chains: | BA_E |
| Organism: | Homo sapiens, Staphylococcus aureus subsp. aureus USA300 |
| Method: | XRD |
| Resolution (Å): | 3.21 |
| Reference: | 10.1038/ncomms13376 |
| Antibody | |
| Antibody: | D4-30-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
| >5D1X_B|Chain B|D4-30 Heavy Chain|Homo sapiens (9606) QVQLVQSGSEVKKPGSSVTLSCKASGDTFNTHTYSWVRQAPGQRLEWIGGIMPIFAASKSAPHLQDRLTITANKATRTAYMELTSLTSDDSGVYYCARDGRGALQYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCGGGSGHHHHHHHHHHGGDYKDHDGDYKDHDIDYKDDDDK |
Light Chain: A
Mutation: NULL
| >5D1X_A|Chain A|D4-30 Light Chain|Homo sapiens (9606) DIVMTQSPLSLPVTLGQPASISCSSAQSLVHSDGDSYLTWFHQRPGQSPRRLIYKVSIRDAGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCMQATHWPYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: E
Mutation: NULL
| >5D1X_E|Chain E|Iron-regulated surface determinant protein B|Staphylococcus aureus (strain USA300) (367830) KMTDLQDTKYVVYESVENNESMMDTFVKHPIKTGMLNGKKYMVMETTNDDYWKDFMVEGQRVRTISKDAKNNTRTIIFPYVEGKTLYDAIVKVHVKTIDYDGQYHVRIVDKEAFTKAN |
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: TYR32 ALA91 THR92 TRP94 TYR96 B: THR28 ASN30 THR31 HIS32 THR33 SER35 TRP47 GLY50 ILE53 PHE54 ALA56 SER57 LYS58 ASP95 GLY96 ARG97 GLY98 ALA99 E: MET362 MET363 THR365 PHE366 ASN388 ASP390 TYR391 ALA409 LYS410 ASN411 ASN412 VAL433 HIS434 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)
