Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 7095 |
| PDBID: | 5D1Z |
| Chains: | BA_I |
| 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: B
Mutation: NULL
| >5D1Z_B|Chain B, H[auth G]|Y10 Heavy Chain|Homo sapiens (9606) AEVQLVESGGGVVQPGGSLRLSCAASGFTFNKFWMNWVRQAPGKGLEWVADIQVDGSEKNYVDSVKGRFTISRDNGKNSLYLQMNSLRAEDTGVYYCARGRYDYWSGYLSPWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCGGGSGHHHHHHHHHHGGDYKDHDGDYKDHDIDYKDDDDK |
Light Chain: A
Mutation: NULL
| >5D1Z_A|Chain A, I[auth H]|Y10 Light Chain|Homo sapiens (9606) DIQMTQSPSFLSASVGDRVTITCRASQGITTYLGWYQQRPGKAPQLLIYAASSLQSGVPPRFSGSGSGTEFTLTISSLQPEDFATYYCQQLNTYPYTFGPGTRLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: I
Mutation: NULL
| >5D1Z_I|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 A: THR32 TYR34 TYR51 ALA52 SER54 SER55 LEU93 ASN94 THR95 TYR98 B: TRP34 GLN53 VAL54 ASP55 SER57 GLU58 ARG101 TYR102 ASP103 TYR104 TRP105 SER106 TYR108 I: ASN119 ASN120 THR121 TYR122 PRO123 ILE124 ASN126 GLN127 GLU131 ALA132 ILE133 LYS134 ASN135 PRO136 ALA137 LYS139 LYS141 TYR214 THR216 |
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)
