Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6141 |
| PDBID: | 8EMZ |
| Chains: | B_A |
| Organism: | Norovirus, Vicugna pacos |
| Method: | XRD |
| Resolution (Å): | 1.40 |
| Reference: | 10.1128/jvi.01833-22 |
| Antibody | |
| Antibody: | 8EMZ_2 VHH |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Noroviruse GII.17 P domain |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: B
Mutation: NULL
| >8EMZ_B|Chain B|Nanobody 2|Vicugna pacos (30538) QVQLQESGGGLVQAGGSLRLSCAASGRFFSSYAMGWFRQAPGKEREFVAAISWSGGSTYYADSVKGRFTTSRDNAKNTVYLLMNSLKPEDTAVYYCAAAREGAYYPDSYYRTVRYDYWGQGTQVTVSS |
Antigen
Chain: A
Mutation: NULL
| >8EMZ_A|Chain A|GII.17 P domain|Norovirus (142786) PFSLPILTLSELTNSRFPVPIDSLFTAQNNVLQVQCQNGRCTLDGELQGTTQLLPTGICAFRGRVTAQINQRDRWHMQLQNLNGTTYDPTDDVPAPLGTPDFKGVVFGMVSQRNVGNDAPGSTRAQQAWVSTYSPQFVPKLGSVNLRISDNDDFQFQPTKFTPVGVNDDDDGHPFRQWELPNYSGELTLNMNLAPPVAPNFPGEQLLFFRSFVPCSGGYNQGIIDCLIPQEWIQHFYQESAPSQSDVALIRYVNPDTGRTLFEAKLHRSGYITVAHSGDYPLVVPANGHFRFDSWVNQFYSLAPM |
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: GLN1 ARG27 PHE28 PHE29 SER30 SER31 TYR32 SER52 TRP53 SER54 GLY56 SER57 TYR59 ASN74 ALA75 ASN77 ARG100 GLU101 GLY102 TYR104 TYR105 PRO106 ASP107 TYR117 A: GLN293 ILE294 ASN295 GLN296 ARG297 ARG299 GLN352 TRP354 ARG372 ILE373 SER374 ASP375 ASN376 ASP377 ASN392 ASP393 ASP395 ASP396 SER441 GLY442 GLY443 TYR444 |
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)
