Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1562 |
| PDBID: | 5M30 |
| Chains: | D_B |
| Organism: | Escherichia coli, Vicugna pacos |
| Method: | XRD |
| Resolution (Å): | 2.60 |
| Reference: | 10.1038/nmicrobiol.2017.103 |
| Antibody | |
| Antibody: | nb18 Nanobody |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Type VI secretion protein |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: D
Mutation: NULL
| >5M30_D|Chain D, E, F|Anti-vesicular stomatitis virus N VHH|Vicugna pacos (30538) QVQLVESGGGLVQAGGTLKLSCAASGSISGIVVMAWYRQAPGKQRELVASITSGGTTNYADSVKGRFTISKDNAENTLYLRMNSLKPEDTAVYYCKAFFRRDYVGYDYWGQGTQVTVSSHHHHHH |
Antigen
Chain: B
Mutation: NULL
| >5M30_B|Chain A, B, C|Type VI secretion protein|Escherichia coli (562) MKIYRPLWEDGAFLMPQQFQQQAAWDVHLADSVARMGLAHPWGVVAAEFDDSLLPLSRLNATRLIVRFPDGTLIDTERADNLPPVCDLSTVSDRSLVDIVLALPLLNANGGNLDNGSESERPRRWKSERVNVQELAGHEQSEVAVLRHNLTLRMAHQENAAWLTCPVTRLVRDAQGQWCRDPRFIPPLLTLSASPSLMTELLELLHHLQARRQRLMSMRRENNARLADFAVADVSLFWLLNALNSAEPVLKELLDMPYRHPELLYRELARLAGSLLTFSLEHNVDAVPAYHHETPENVFPPLLSLLNRLLEASLPSRVVFIELKQKGVMWEGALHDARLREGADFWLSVRSSMPGHELQTKFPQLCKAGSPDDVSEVVNVALSGVIIRPVTHVPAAIPLRLENQYFALDLSTDAARAMLDAGRCTFYTPASLGDVKLELFAVLRT |
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: VAL32 VAL33 ALA35 TYR37 ARG45 LEU47 SER50 THR52 SER53 GLY54 THR56 ALA60 LYS96 PHE98 ARG100 TYR103 VAL104 GLY105 TYR106 ASP107 TYR108 B: ARG35 TRP42 PRO69 ASP70 LEU105 LEU106 ASN107 ALA108 ASN109 GLY110 SER117 GLU118 SER119 GLU120 ARG121 GLU158 ALA160 ALA161 TRP162 LEU163 |
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)
