Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1623 |
| PDBID: | 5O05 |
| Chains: | D_A |
| Organism: | Vicugna pacos, Norwalk virus |
| Method: | XRD |
| Resolution (Å): | 2.00 |
| Reference: | 10.1371/journal.ppat.1006636 |
| Antibody | |
| Antibody: | Nano-42 Nanobody |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Norwalk virus Capsid protein |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: D
Mutation: NULL
| >5O05_D|Chain A[auth C], B[auth D]|Nanobody (VHH) Nano-42|Vicugna pacos (30538) QVQLQESGGGLVQPGGSLRLSCAASGSVSRTYVMGWYRQTPGNQRELVATITSVGSTNYADSLKGRFTISRENAENTVYLQMNSLKPEDTAIYYCKYIRYSPIHAPLDYWGQGTQVTVSS |
Antigen
Chain: A
Mutation: NULL
| >5O05_A|Chain C[auth A], D[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)
| D: THR31 VAL33 TYR37 LEU47 THR50 THR52 SER53 VAL54 SER56 THR57 ASN58 LYS96 ILE98 TYR100 SER101 PRO102 ILE103 HIS104 ALA105 PRO106 ASP108 A: PRO226 PHE227 LEU477 SER478 LEU482 ARG484 GLU496 PHE525 ASP526 SER527 TRP528 VAL529 ASN530 PHE532 TYR533 THR534 LEU535 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)
