Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1955 |
| PDBID: | 5XBM |
| Chains: | ED_F |
| Organism: | Mus musculus, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 3.50 |
| Reference: | 10.1007/s13238-017-0405-7 |
| Antibody | |
| Antibody: | JL2 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Lysosome membrane protein 2 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: E
Mutation: NULL
| >5XBM_E|Chain B, E|heavy chain of JL2|Mus musculus (10090) EVQLQQSGPELEKPGASVKISCMASGYSFTGYNMNWVKQSNGKSLEWIGNIDPYYGDTRYNQKFKDKATLTVDKSSSTAYMQLKSLTSEDSAVYYCARSRGSTSYFYGMDYWGQGTSVTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPALLQSGLYTLSSSVTVTSNTWPSQTITCNVAHPASSTKVDKKIEPR |
Light Chain: D
Mutation: NULL
| >5XBM_D|Chain A, D|light chain of JL2|Mus musculus (10090) CDIVMTQSPATLSVTPGDRVSLSCRASQSISDYLHWYQQKSHESPRLLIKYQSISGIPSRFSGSGSGSDFTLSINSVEPEDVGVYYCQNGHSFPFTFGSGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC |
Antigen
Chain: F
Mutation: NULL
| >5XBM_F|Chain C, F|Lysosome membrane protein 2|Homo sapiens (9606) IEKKIVLRNGTEAFDSWEKPPLPVYTQFYFFNVTNPEEILRGETPRVEEVGPYTYRELRNKANIQFGDNGTTISAVSNKAYVFERDQSVGDPKIDLIRTLNIPVLTVIEWSQVHFLREIIEAMLKAYQQKLFVTHTVDELLWGYKDEILSLIHVFRPDISPYFGLFYEKNGTNDGDYVFLTGEDSYLNFTKIVEWNGKTSLDWWITDKCNMINGTDGDSFHPLITKDEVLYVFPSDFCRSVYITFSDYESVQGLPAFRYKVPAEILANTSDNAGFCIPEGNCLGSGVLNVSICKNGAPIIMSFPHFYQADERFVSAIEGMHPNQEDHETFVDINPLTGIILKAAKRFQINIYVKKLDDFVETGDIRTMVFPVMYLNESVHIDKETASRLKSMIN |
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)
| D: ASP31 TYR32 LYS49 TYR50 SER52 E: TYR27 SER28 THR30 GLY31 TYR32 ASP52 TYR54 TYR55 ARG100 GLY101 SER102 THR103 TYR105 TYR107 F: GLU73 LEU76 ARG77 GLU79 GLU157 LEU160 LYS161 GLN164 GLN165 LYS166 LYS391 ASP393 ASP394 PHE395 VAL396 GLU397 GLY399 ASP400 |
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)
