Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 7160 |
| PDBID: | 5NBL |
| Chains: | F_D |
| Organism: | Saccharomyces cerevisiae S288C, Vicugna pacos, Trichoplusia ni |
| Method: | XRD |
| Resolution (Å): | 2.80 |
| Reference: | 10.1038/s41594-018-0115-8 |
| Antibody | |
| Antibody: | Nact Nanobody |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Actin-related protein Arp4–N-actin (apo) |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: F
Mutation: NULL
| >5NBL_F|Chain E, F|nAct-Nanobody|Vicugna pacos (30538) MAQVQLVESGGGSVQAGDSLRLSCTASGRTFTNYGMGWFRQAPGKEREFVAAIGRFGFPLYYSDSVKGRFTISRDNAKTTVYLQMHNLKPEDTAIYFCAARNPRATAEDVSAYDYWGQGTQVTVSSKGSSAWSHPQFEKGGGSGGGSGGSAWSHPQFEK |
Antigen
Chain: D
Mutation: NULL
| >5NBL_D|Chain C, D|Actin|Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (559292) MDSEVAALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGIMVGMGQKDSYVGDEAQSKRGILTLRYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPMNPKSNREKMTQIMFETFNVPAFYVSIQAVLSLYSSGRTTGIVLDSGDGVTHVVPIYAGFSLPHAILRIDLAGRDLTDYLMKILSERGYSFSTTAEREIVRDIKEKLCYVALDFEQEMQTAAQSSSIEKSYELPDGQVITIGNERFRAPEALFHPSVLGLESAGIDQTTYNSIMKCDVDVRKELYGNIVMSGGTTMFPGIAERMQKEITALAPSSMKVKIIAPPERKYSVWIGGSILASLTTFQQMWISKQEYDESGPSIVHHKCF |
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)
| F: ARG29 THR32 ASN33 ARG55 PHE56 PHE58 PRO59 TYR61 LYS67 ASN76 ASN102 PRO103 ARG104 ALA105 THR106 ALA107 GLU108 ASP109 SER111 ALA112 ASP114 D: SER14 GLY15 ARG39 ARG62 LEU65 THR66 LEU67 ARG68 TYR69 GLU72 THR77 ASP157 GLY158 ARG177 ASP179 ARG183 ASP184 ASP187 TYR188 MET190 LYS191 PHE200 SER201 THR202 THR203 ARG206 LEU267 GLY268 LEU269 |
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)
