Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 3239 |
| PDBID: | 6XW4 |
| Chains: | D_B |
| Organism: | Murine norovirus 1, Vicugna pacos |
| Method: | XRD |
| Resolution (Å): | 2.19 |
| Reference: | 10.1128/JVI.00660-20 |
| Antibody | |
| Antibody: | NB-5867 Nanobody |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | murine norovirus P domain |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: D
Mutation: NULL
| >6XW4_D|Chain C, D|Nanobody NB-5867|Vicugna pacos (30538) QVQLQESGGGLVQAGGSLRLSCAKSGRTFRAYAMGWFRQAPGKEREFVAAIDWSAAITNYADSVKGRFTILRDKGMNTAYLQMNSLEPEDTAVYYCAATYSTIAPRTSYDFWGQGTQVTVSSHHHHHH |
Antigen
Chain: B
Mutation: NULL
| >6XW4_B|Chain A, B|Capsid protein|Murine norovirus 1 (223997) RMVDLPVIQPRLCTHARWPAPVYGLLVDPSLPSNPQWQNGRVHVDGTLLGTTPISGSWVSCFAAEAAYKFQSGTGEVATFTLIEQDGSAYVPGDRAAPLGYPDFSGQLEIEVQTETTKTGDKLKVTTFEMILGPTTNADQAPYQGRVFASVTAAASLDLVDGRVRAVPRSIYGFQDTIPEYNDGLLVPLAPPIGPFLPGEVLLRFRTYMRQIDTADAAAEAIDCALPQEFVSWFASNAFTVQSEALLLRYRNTLTGQLLFECKLYNEGYIALSYSGSGPLTFPTDGIFEVVSWVPRLYQLASVGSL |
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: LYS24 GLY26 ARG27 THR28 PHE29 ARG30 ALA31 TYR32 ASP52 TRP53 SER54 ALA56 ILE57 LYS74 GLY75 MET76 ASN77 TYR100 THR102 ASP110 PHE111 B: LYS296 GLN298 GLY300 THR301 VAL304 GLY333 GLN334 GLU356 ILE358 GLY360 PRO361 THR362 THR363 ASN364 ALA365 ASP366 ARG373 PHE375 ALA376 SER377 VAL378 THR379 TYR399 GLY400 PHE401 GLN402 ILE439 ASP440 THR441 |
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)
