Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 3241 |
| PDBID: | 6XW6 |
| Chains: | D_B |
| Organism: | Murine norovirus 1, Vicugna pacos |
| Method: | XRD |
| Resolution (Å): | 1.96 |
| Reference: | 10.1128/JVI.00660-20 |
| Antibody | |
| Antibody: | NB-5853 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
| >6XW6_D|Chain C, D|Nanobody NB-5853|Vicugna pacos (30538) QVQLQESGGGLVQAGDSLRVSCAASGRTISSSPMGWFRQAPGKEREFVAAISGNGGNTYYLDSVKGRFTTSRDNAKNTVYLQLNNLKPEDTAIYYCAARSRFSAMHLAYRRLVDYDDWGQGTQVTVSSHHHHHH |
Antigen
Chain: B
Mutation: NULL
| >6XW6_B|Chain A, B|Capsid protein|Murine norovirus 1 (223997) SRMVDLPVIQPRLCTHARWPAPVYGLLVDPSLPSNPQWQNGRVHVDGTLLGTTPISGSWVSCFAAEAAYKFQSGTGEVATFTLIEQDGSAYVPGDRAAPLGYPDFSGQLEIEVQTETTKTGDKLKVTTFEMILGPTTNADQAPYQGRVFASVTAAASLDLVDGRVRAVPRSIYGFQDTIPEYNDGLLVPLAPPIGPFLPGEVLLRFRTYMRQIDTADAAAEAIDCALPQEFVSWFASNAFTVQSEALLLRYRNTLTGQLLFECKLYNEGYIALSYSGSGPLTFPTDGIFEVVSWVPRLYQLASVGSL |
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: SER31 PRO33 PHE47 ASN54 ASN57 TYR59 LEU61 ASP62 ARG99 SER100 ARG101 PHE102 SER103 ALA104 MET105 HIS106 LEU107 TYR109 ARG110 ARG111 VAL113 ASP114 ASP116 B: GLY300 THR301 VAL304 GLY333 GLN334 GLU356 ILE358 GLY360 PRO361 THR362 THR363 ASN364 ALA365 PHE375 ALA376 SER377 THR379 TYR399 GLY400 GLN402 ILE439 ASP440 THR441 ALA442 ASP443 |
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)
