Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 7093 |
| PDBID: | 5D1Z |
| Chains: | FE_J |
| Organism: | Homo sapiens, Staphylococcus aureus subsp. aureus MSSA476 |
| Method: | XRD |
| Resolution (Å): | 3.17 |
| Reference: | 10.1038/ncomms13376 |
| Antibody | |
| Antibody: | D4-10-N1 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Iron-regulated surface determinant protein B (IsdB) NEAT1 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: F
Mutation: NULL
| >5D1Z_F|Chain D, G[auth F]|D4-10 Heavy Chain|Homo sapiens (9606) QVQLQESGPGLVKPSETLSLICTVSGGSISSSSYYWGWIRQTPERNLEWIGIIYFSGTTYYNPSLQSRVSMSLDRSTNRFSLRLSSVTAADTAIYYCAKPKSRDRGGPGDDYFGMDVWGQGIMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCGGGSGHHHHHHHHHHGGDYKDHDGDYKDHDIDYKDDDDK |
Light Chain: E
Mutation: NULL
| >5D1Z_E|Chain C, F[auth E]|D4-10 Light Chain|Homo sapiens (9606) DIQLTQSPSFLSASVADRVTITCRASQAVRSSLAWYQQKPGKAPQLLIYSASTLENGVSSRFSGSGPGTEFTLTISSLQPEDVGTYYCQQLNTYPFTFGPGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: J
Mutation: NULL
| >5D1Z_J|Chain E[auth I], J|Iron-regulated surface determinant protein B|Staphylococcus aureus (strain MSSA476) (282459) GPAKATNNTYPILNQELREAIKNPAIKDKDHSAPNSRPIDFEMKKKDGTQQFYHYASSVKPARVIFTDSKPEIELGLQSGQFWRKFEVYEGDKKLPIKLVSYDTVKDYAYIRFSVSNGTKAVKIVSSTHFNNKEEKYDYTLMEFAQPIYNSADKFKT |
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 E: ARG32 LEU93 ASN94 THR95 TYR96 PHE98 F: SER31 SER33 TYR34 ILE52 TYR54 PHE55 SER56 THR58 THR59 TYR60 ARG75 ARG103 GLY107 PRO108 GLY109 ASP110 TYR112 J: LYS157 ASP159 THR161 GLN162 GLN163 PHE164 TYR165 TYR167 ALA168 SER169 GLN190 SER191 GLN193 PHE194 ASP219 THR240 HIS241 PHE242 ASN243 GLU247 TYR249 |
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)
