Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 4617 |
| PDBID: | 7PIJ |
| Chains: | N_B |
| Organism: | synthetic construct, Staphylococcus capitis, Lama glama |
| Method: | EM |
| Resolution (Å): | 3.78 |
| Reference: | 10.1073/pnas.2115435118 |
| Antibody | |
| Antibody: | DMTNb16_4 Nanobody |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | bacterial divalent metal ion transporter ScaDMT |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: N
Mutation: NULL
| >7PIJ_N|Chain D[auth N]|DMTNb16_4|synthetic construct (32630) QRQLVESGGGLVQPGGSLRLSCAASRSIFSIDTAGWFRQAPGKEREGVATITRDGNANYADSVKGRFTISRDRARNTVYLQMNSLEPEDTAVYYCNAAIRTTVRTSAQEYWGKGTPVTVSSHHHHHHEPEA |
Antigen
Chain: B
Mutation: NULL
| >7PIJ_B|Chain C[auth B]|Divalent metal cation transporter MntH|Staphylococcus capitis (29388) MSVAVGYMDPGNWITSMQGGAQYGYTLLFVILISSLAAMLLQSMTVRLGIATGKDLAQMTRHFLSKPVAIIFWIIAELAIIATDIAEVIGSAIALDLIFGIPLIVGALITVFDVFLLLFIMRFGFRKIEAIVGTLIFTVLAIFVFEVFISSPQLTDILNGFVPHKEIVTNQGILYIALGIIGATIMPHNLYLHSSIVQSRKYDRHDNQEKAQAIKYATIDSNLQLSIAFVVNCLLLTLGAALFFGTKTNDLGGFYDLYHALKTEPVLGATLGGIMSTLFAVALLASGQNSTITGTLAGQIVMEGFLRLSIPNWLRRLITRALAVIPVIICLIIFKGNSEKIEQLLVFSQVFLSIALPFSLIPLQLATSNKKLMGPFINKTWVNIISWTLIVILSGLNVYLIIQTFQELALEVLFQGPHHHHHHHHHH |
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)
| N: SER27 ILE28 PHE29 ASP32 ARG53 ASP54 GLY55 ARG71 ARG73 ALA74 ARG75 ASN76 ARG97 THR98 THR99 B: ASP136 LEU137 ILE138 PHE139 GLY140 ALA280 ALA281 LEU282 PHE283 PHE284 GLY285 THR286 LYS287 THR288 ASP290 TYR295 ASP296 TYR298 HIS299 ALA300 LYS302 THR303 PRO305 ASN377 SER378 GLU379 LYS380 |
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)
