Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 3987 |
| PDBID: | 7KPJ |
| Chains: | AB_E |
| Organism: | Mus musculus, Mediterraneibacter gnavus |
| Method: | XRD |
| Resolution (Å): | 2.10 |
| Reference: | 10.1073/pnas.2023898118 |
| Antibody | |
| Antibody: | 338E6 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Ruminococcus gnavus immunoglobulin binding protein |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: A
Mutation: NULL
| >7KPJ_A|Chain D[auth A], E[auth C]|338E6 Fab heavy chain|Mus musculus (10090) EVKLEESGGDLVKPGGSLKLSCAASGFTFSSYGMSWVRQTPDKRLEWVATISSGGSYTYYPDSVKGRFTISRDNAKNTLYLQMSSLKSEDTAMYYCARRGFYFDYWGQGTTLTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT |
Light Chain: B
Mutation: NULL
| >7KPJ_B|Chain A[auth B], F[auth D]|338E6 Fab light chain kappa|Mus musculus (10090) ETTVTQSQKFMSTSVGDRVSVTCKASQNVGTNVAWYQQKPGQSPKALIYSASYRYSGVPDRFTGSGSGTDFTLTISNVQSEDLAEYFCQQYNSYPLTFGQGTKVEIKRTVAAPSVFIFPPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: E
Mutation: NULL
| >7KPJ_E|Chain B[auth E], C[auth F]|GRAM_POS_ANCHORING domain-containing protein|Ruminococcus gnavus (33038) HHHHHHVAEAPAEEVQNVKINYYDEDAEKQVAEVPVQVSIDTSCVNMAILTRYMPEGYALVSSDCIIRDGYVYVSVKKDVEIREAVLHITFETPNGEVVTTETVTAEGADGEDAVFRLGVDFNLPTGYKLSNDRDQVTEITIPFGSTGGHTMVVEKGDLSSIVKIQFVDAENNDEVVAGGDYFVDGDGDGIFHTREITEWVPEGYELQEVGDFQVELYKETPLQLSVTKIKEDKPETPDPEEPNKPEDPDKEDTNNKDDKKEDTKKEDKKKN |
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 B: SER7 GLN8 MET11 SER12 THR13 GLY16 ARG18 VAL19 SER20 THR22 CYS23 LYS24 ASP60 SER65 ASP70 PHE71 THR72 THR74 SER76 ASN77 GLN79 LYS107 E: ASP34 THR35 SER36 CYS37 CYS58 ILE59 ILE60 ARG61 ASP62 ARG110 LEU111 GLY112 VAL113 LEU117 LYS122 LEU123 ASN125 ASP128 GLN129 THR131 GLU132 |
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)
