Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 3944 |
| PDBID: | 7KGV |
| Chains: | DF_A |
| Organism: | Danio rerio, Mus musculus |
| Method: | XRD |
| Resolution (Å): | 3.40 |
| Reference: | 10.1016/j.str.2020.11.014 |
| Antibody | |
| Antibody: | 7KGV Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | sodium-coupled neutral amino acid transporter SLC38A9 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: D
Mutation: NULL
| >7KGV_D|Chain C, D|Monoclonal antibody Fab heavy chain|Mus musculus (10090) QIQLVQSGPKLSKPGATDKISCAAGGYSFTDYVMNWVKASPLKGLEWNGSINTSNGATTYISAFKGAGSHSVDSSASTAAQQLSALKAADTAVYFCARNFRGNGAMDYWGQGTSVTVSSAKTTAPSVYPLEVSAAXATGSSVTLGCLVKGYFPEPCTLTWNSGSLSSGVHTFPAVLASDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPA |
Light Chain: F
Mutation: NULL
| >7KGV_F|Chain E, F|Monoclonal antibody Fab light chain|Mus musculus (10090) DILLTQSPESLSVVVGFYVTITSQASNNITTYSSFIFWYQQKPGQAPKLLIYDSSTLESGIPGRFSGSGSGRDFSLTIAPNQPACGATYEDLQVLIVVRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGAEVVCFLNNFYPKNINVAWKIDGGERQNGVLNSWTDQDSADSTYSMSSTLTLTKDEYERHASYTCEATHQTSTSPIVKSFNRN |
Antigen
Chain: A
Mutation: NULL
| >7KGV_A|Chain A, B|Sodium-coupled neutral amino acid transporter 9|Danio rerio (7955) MDEDSKPLLGSVPTGDYYTDSLDPKQRRPFHVEPRNIVGEDVQERVSAEAAVLSSRVHYYSRLTGSSDRLLAPPDHVIPSHEDIYIYSPLGTAFKVQGGDSPIKNPSIVTIFAIWNTMMGTSILSIPWGIKQAGFTLGIIIIVLMGLLTLYCCYRVLKSTKSIPYVDTSDWEFPDVCKYYFGGFGKWSSLVFSLVSLIGAMVVYWVLMSNFLFNTGKFIFNYVHNVQTSDAFGTQGTERVICPYPDVDPHGQSSTSLYSGSDQSTGLEFDHWWSKTNTIPFYLILLLLPLLNFRSASFFARFTFLGTISVIYLIFLVTYKAIQLGFHLEFHWFDSSMFFVPEFRTLFPQLSGVLTLAFFIHNCIITLMKNNKHQENNVRDLSLAYLLVGLTYLYVGVLIFAAFPSPPLSKECIEPNFLDNFPSSDILVFVARTFLLFQMTTVYPLLGYLVRVQLMGQIFGNHYPGFLHVFVLNVFVVGAGVLMARFYPNIGSIIRYSGALCGLALVFVLPSLIHMVSLKRRGELRWTSTLFHGFLILLGVANLLGQFFM |
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 D: TYR27 SER28 ASP31 TYR32 VAL33 TRP47 SER50 ASN52 SER54 ASN55 ALA57 THR58 THR59 ASN99 PHE100 ARG101 GLY102 ASN103 F: THR31 TYR32 SER33 PHE35 ASP53 VAL94 LEU95 ILE96 VAL97 ARG99 A: GLU238 ARG239 VAL240 ILE241 CYS242 PRO243 TYR244 PRO245 LEU324 HIS327 GLU329 SER335 SER336 MET337 PHE338 PHE339 VAL340 PRO341 ARG344 PRO404 PRO406 PRO407 LEU408 SER409 GLU411 CYS412 |
2、We defined interacting paratope-epitope residues by a distance cutoff of < 6 Å . Two amino acids are considered as interacting residues if they have at least one atom within a distance of 6 Å from any atom.
Interacting residues (Atom distance based)
