Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1567 |
| PDBID: | 5M95 |
| Chains: | B_A |
| Organism: | Staphylococcus capitis, Lama glama |
| Method: | XRD |
| Resolution (Å): | 3.40 |
| Reference: | 10.1038/nsmb.2904 |
| Antibody | |
| Antibody: | 5M95 Nanobody |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Divalent metal cation transporter MntH |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: B
Mutation: NULL
| >5M95_B|Chain B, C[auth D]|CAMELID ANTIBODY FRAGMENT, NANOBODY|Lama glama (9844) GPSQVQLQESGGGLVQAGGSLRLSCAASRSIFSIDTANWYRQPPGMQRELVATITRDGNANYADSVKGRFTISRDRARNTVYLQMNSLKPEDTGVYYCNAAIRTTVRTSAQEYWGQGTQVTVSS |
Antigen
Chain: A
Mutation: NULL
| >5M95_A|Chain A, D[auth C]|Divalent metal cation transporter MntH|Staphylococcus capitis (29388) MSVAVGYMDPGNWITSMQGGAQYGYTLLFVILISSLAAMLLQSMTVRLGIATGKDLAQMTRHFLSKPVAIIFWIIAELAIIATDIAEVIGSAIALDLIFGIPLIVGALITVFDVFLLLFIMRFGFRKIEAIVGTLIFTVLAIFVFEVFISSPQLTDILNGFVPHKEIVTNQGILYIALGIIGATIMPHNLYLHSSIVQSRKYDRHDNEEKAQAIKYATIDSNLQLSIAFVVNCLLLTLGAALFFGTKTNDLGGFYDLYHALKTEPVLGATLGGVMSTLFAVALLASGQNSTITGTLAGQIVMEGFLRLSIPNWLRRLITRSLAVIPVIICLIIFKGNSEKIEQLLVFSQVFLSIALPFSLIPLQLATSNKKLMGPFINKTWVNIISWTLIVILSGLNVYLIIQTFQELALEVLFQ |
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)
| B: SER27 ILE28 PHE29 ASP32 ARG53 ASP54 GLY55 THR68 ASP72 ARG73 ALA74 ARG75 ASN76 ARG100 THR101 THR102 VAL103 ARG104 SER106 ALA107 A: ASP136 LEU137 ILE138 PHE139 GLY140 ALA281 LEU282 PHE283 PHE284 GLY285 THR286 LYS287 THR288 ASN289 ASP290 LEU291 TYR295 ASP296 TYR298 HIS299 ALA300 LYS302 THR303 GLU304 PRO305 ALA309 LYS375 ASN377 SER378 GLU379 |
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)
