Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1636 |
| PDBID: | 5OMN |
| Chains: | C_B |
| Organism: | Norwalk virus, Vicugna pacos |
| Method: | XRD |
| Resolution (Å): | 2.68 |
| Reference: | 10.1371/journal.ppat.1006636 |
| Antibody | |
| Antibody: | Nano-27 Nanobody |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Norwalk virus Capsid protein |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: C
Mutation: NULL
| >5OMN_C|Chain B[auth C]|Nanobody (VHH) Nano-27|Vicugna pacos (30538) QVQLQESGGGLVQPGGSLRLSCAASGTIFSRNIMGWYRQAPGKERELVASIYSDRSTWYAESVEGRFTISRDNVKNTLYLQMNSLKPEDTAMYYCRDRTLGSWGQGTQVTVSSHHHHHH |
Antigen
Chain: B
Mutation: NULL
| >5OMN_B|Chain A[auth B]|Capsid protein|Norwalk virus (11983) SKPFTLPILTLGELTNSRFPLPIDVLYTNPNESAIVQCQNGRCTLDGELQGTTQLLPTGICAFRGKVTQQVQDEHRGTHWNMTVTNLNGTPFDPTEDVPAPLGTPDFSGQIYGVISQRNTNTVPGEGNLPANRAHEAVIATYSPKFTPKLGNIQFSTWETQDVSSGQPTKFTPVGLASVDANSHFDQWTLPSYSGALTLNMNLAPSVAPVFPGECLLFFRSFIPLKGGYGNPAIDCLMPQEWVQHLYQESAPSLSDVALVRYVNPETGRTLFEAKLHRNGFLTVARNSAGPVVAPTNGYFRFDSWVNQFYTLAPM |
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)
| C: ILE33 TYR37 LEU47 TYR52 SER53 ASP54 SER56 THR57 TRP58 TYR59 GLU64 ARG96 ARG98 THR99 LEU100 B: LEU482 ARG484 GLY491 ARG492 THR493 LEU494 PHE495 GLU496 ARG524 ASP526 SER527 VAL529 ASN530 PHE532 TYR533 THR534 ALA536 PRO537 |
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)
