Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 7089 |
| PDBID: | 5D1Q |
| Chains: | CD_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: C
Mutation: NULL
| >5D1Q_C|Chain C|P5 Heavy Chain|Homo sapiens (9606) EVQLVESGGGLVQPGGSLTLSCAASGLIFSDSTMHWVRQASGRGLEWVARIRSKANNYATSSDKSATAYLASVKGRFTISRDDSKDTTFLEMSSLKIEDTAVYYCIASSTTGWYVREDFDYWGHGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCGGGSGHHHHHHHHHHGGDYKDHDGDYKDHDIDYKDDDDK |
Light Chain: D
Mutation: NULL
| >5D1Q_D|Chain D|P5 Light Chain|Homo sapiens (9606) EIVLTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLSISRLEPEDFAVYYCLHYGTSPMYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
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 C: THR97 GLY99 D: VAL29 SER30 SER31 TYR32 GLY50 SER52 SER53 ARG54 ASP60 GLY66 SER67 GLY68 E: LYS341 MET342 THR343 ASP344 LEU345 GLN346 ASP347 LYS368 PRO370 LYS372 VAL383 GLU385 ILE405 SER406 LYS410 ASN411 THR415 |
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)
