Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1349 |
| PDBID: | 5FOJ |
| Chains: | A_B |
| Organism: | Camelus dromedarius, Grapevine fanleaf virus |
| Method: | EM |
| Resolution (Å): | 2.80 |
| Reference: | 10.1073/pnas.1913681117 |
| Antibody | |
| Antibody: | Nb23 Nanobody |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Grapevine Fanleaf Virus RNA2 polyprotein |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: A
Mutation: NULL
| >5FOJ_A|Chain A|Nanobody|Camelus dromedarius (9838) QVQLQESGGGSVQVGGSLRVACAASGDTFSGYLAAWFRQAPGKGREGVAAINSKRHTTSYADSVKGRFTISKDNADNIMYLEMNSLKPEDTAIYYCAAADAIGLAEYWSTPTLSAARYKYWGQGTQVTVSSHHHHHH |
Antigen
Chain: B
Mutation: NULL
| >5FOJ_B|Chain B|RNA2 polyprotein|Grapevine fanleaf virus (12274) GLAGRGVIYIPKDCQANRYLGTLNIRDMISDFKGVQYEKWITAGLVMPTFKIVIRLPANAFTGLTWVMSFDAYNRITSRITASADPVYTLSVPHWLIHHKLGTFSCEIDYGELCGHAMWFKSTTFESPRLHFTCLTGNNKELAADWQAVVELYAELEEATSFLGKPTLVFDPGVFNGKFQFLTCPPIFFDLTAVTALRSAGLTLGQVPMVGTTKVYNLNSTLVSCVLGMGGTVRGRVHICAPIFYSIVLWVVSEWNGTTMDWNELFKYPGVYVEEDGSFEVKIRSPYHRTPARLLAGQSQRDMSSLNFYAIAGPIAPSGETAQLPIVVQIDEIVRPDLSLPSFEDDYFVWVDFSEFTLDKEEIEIGSRFFDFTSNTCRVSMGENPFAAMIACHGLHSGVLDLKLQWSLNTEFGKSSGSVTITKLVGDKAMGLDGPSHVFAIQKLEGTTELLVGNFAGANPNTRFSLYSRWMAIKLDQAKSIKVLRVLCKPRPGFSFYGRTSFPV |
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)
| Chain residues position delta_SASA
: residuesposition A: PHE29 TYR32 LYS54 ARG55 THR57 THR58 ASP62 LYS65 ASP100 ALA101 ILE102 GLY103 LEU104 ALA105 TYR107 TRP108 SER109 THR110 PRO111 THR112 LEU113 B: ARG79 MET209 GLY211 THR212 THR213 LYS214 TYR216 THR357 LEU358 PHE370 ASP371 PHE372 THR373 SER374 ASN375 THR376 CYS377 ARG378 VAL379 SER380 MET381 GLY382 GLU383 ALA387 ALA388 ALA391 ASN461 PHE502 VAL504 |
2、We defined interacting paratope-epitope residues by a distance cutoff of < 6 Å . Two amino acids are considered as interacting residues if they have at least one atom within a distance of 6 Å from any atom.
Interacting residues (Atom distance based)
