Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6418 |
| PDBID: | 8J7E |
| Chains: | AB_F |
| Organism: | Homo sapiens, Escherichia coli |
| Method: | XRD |
| Resolution (Å): | 2.80 |
| Reference: | 10.1038/s41589-023-01389-0 |
| Antibody | |
| Antibody: | 1b3 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Escherichia coli soluble cytochrome b562: BRIL |
| Antigen mutation: | No |
| Durg Target: | P0ABE7 |
Sequence information
Antibody
Heavy Chain: A
Mutation: NULL
| >8J7E_A|Chain A, C|Antibody 1b3 Fab Heavy chain|Homo sapiens (9606) EVQLVESGGGLVQPGGSLRLSCAASGFNIYYSSMHWVRQAPGKGLEWVASISPYSGSTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARPWYPWSYWSGLDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCGSLEHHHHHH |
Light Chain: B
Mutation: NULL
| >8J7E_B|Chain B, D|Antibody 1b3 Fab Light chain|Homo sapiens (9606) MKYLLPTAAAGLLLLAAQPAMADIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQPWSWGSALITFGQGTKVEIKRTVAAPSVFIFPPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG |
Antigen
Chain: F
Mutation: NULL
| >8J7E_F|Chain E, F|Soluble cytochrome b562|Escherichia coli (562) ADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYL |
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)
| A: TYR33 TYR34 SER55 TYR57 SER58 SER60 TYR62 ASP65 PRO105 TRP106 SER107 TYR108 TRP109 SER110 B: GLN28 SER29 SER31 ALA33 TRP93 SER94 TRP95 GLY96 SER97 LEU99 F: TRP7 ASP60 PHE61 HIS63 GLY64 PHE65 ASP66 ILE67 LEU68 GLY70 GLN71 ASP73 ASP74 LYS77 LEU78 GLU81 LYS83 GLU86 ALA89 ALA90 GLN93 THR96 THR97 ASN99 ALA100 TYR101 GLN103 LYS104 TYR105 |
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)
