Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6274 |
| PDBID: | 8GPT |
| Chains: | DE_A |
| Organism: | Yellow fever virus, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 3.07 |
| Reference: | 10.1016/j.xinn.2022.100323 |
| Antibody | |
| Antibody: | YD6 Fv |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Yellow fever virus soluble E protein (YFV-sE) |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: D
Mutation: NULL
| >8GPT_D|Chain B[auth D], E[auth F], H|YD6_VH|Homo sapiens (9606) EVQLVESGGGLVKPGGSLRLSCAASGFIFSDYYMMWIRQAPGKGLEWISYISSSGSQIYYTESVKGRFTISRDNGKNLLYLQMNSLRGEDTALYYCATETGWRIDTWGQGTLVTVSS |
Light Chain: E
Mutation: NULL
| >8GPT_E|Chain C[auth E], F[auth G], I|YD6_VL|Homo sapiens (9606) QAVLTQPASVSGSPGQSITISCTGTGSNIETYNLVSWYQRHPGKAPKLILYEVSERPSGVSNRFSGSKSGNTASLTISGLQAEDEADYFCCSYADTNIFWVFGGGTHLTVLG |
Antigen
Chain: A
Mutation: NULL
| >8GPT_A|Chain A, D[auth B], G[auth C]|Envelope protein|Yellow fever virus (11089) AHCIGITDRDFIEGVHGGTWVSATLEQDKCVTVMAPDKPSLDISLQTVAIDGPAEARKVCYSAVLTHVKINDKCPSTGEAHLAEENDGDNACKRTYSDRGWGNGCGLFGKGSIVACAKFTCAKSMSLFEVDQTKIQYVIRAQLHVGAKQENWNTDIKTLKFDALSGSQEAEFTGYGKATLECQVQTAVDFGNSYIAEMEKDSWIVDRQWAQDLTLPWQSGSGGIWREMHHLVEFEPPHAATIRVLALGNQEGSLKTALTGAMRVTKDENDNNLYKLHGGHVSCRVKLSALTLKGTSYKMCTDKMSFVKNPTDTGHGTVVMQVKVPKGAPCKIPVIVADDLTAAVNKGILVTVNPIASTNDDEVLIEVNPPFGDSYIIVGTGDSRLTYQWHKEGSSIGK |
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 D: SER30 ASP31 TYR32 TYR33 TYR50 SER52 SER53 SER54 SER56 GLN57 TYR59 GLU99 THR100 GLY101 TRP102 E: THR31 TYR32 LEU34 GLU52 TYR93 THR96 PHE99 TRP100 A: VAL64 LEU65 THR66 HIS67 VAL68 LYS69 ILE70 ASN71 ASP72 LYS73 HIS81 LEU82 ALA83 GLU84 ASP87 ASN90 CYS116 ALA117 LYS118 THR120 ALA240 THR241 |
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)
