Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1032 |
| PDBID: | 4X7C |
| Chains: | D_B |
| Organism: | Norovirus Hu/GII-4/Saga1/2006/JP, Vicugna pacos |
| Method: | XRD |
| Resolution (Å): | 2.00 |
| Reference: | 10.1128/JVI.03176-14 |
| Antibody | |
| Antibody: | Nano-85 Nanobody |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | VP1(Saga-2006 GII.4 P domain) |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: D
Mutation: NULL
| >4X7C_D|Chain C, D|Nano-85 Nanobody|Vicugna pacos (30538) DVQLVESGGGLVQPGGSLRLSCAASGSIFSIYAMGWYRQAPGKQRELVASISSGGGTNYADSVKGRFTISGDNAKNTVYLQMNSLKPEDTAVYYCKREDYSAYAPPSGSRGRGTQVTVSSHHHHHH |
Antigen
Chain: B
Mutation: NULL
| >4X7C_B|Chain A, B|VP1|Norovirus Hu/GII-4/Saga1/2006/JP (546980) SKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFVVQPQNGRCTTDGVLLGTTQLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGLLTQTTKGDGSTRGHKATVYTGSAPFTPKLGSVQFSTDTENDFETHQNTKFTPVGVIQDGSTTHRNEPQQWVLPSYSGRNVHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLDCLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLVIPPNGYFRFDSWVNQFYTLAPM |
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: ILE31 TYR32 ALA33 MET34 GLY35 TYR37 ARG45 LEU47 SER50 SER52 SER53 GLY54 GLY55 GLY56 THR57 ASN58 LYS64 LYS96 GLU98 TYR100 SER101 ALA102 TYR103 ALA104 PRO105 PRO106 B: SER224 PRO226 PHE227 PHE426 PRO427 GLN469 SER470 LEU474 ARG476 GLU488 PHE517 ASP518 SER519 TRP520 VAL521 ASN522 GLN523 PHE524 TYR525 THR526 LEU527 ALA528 PRO529 |
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)
