Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 7348 |
| PDBID: | 7PAA |
| Chains: | T_D |
| Organism: | Homo sapiens, JC polyomavirus |
| Method: | XRD |
| Resolution (Å): | 3.10 |
| Reference: | Not available or To be published |
| Antibody | |
| Antibody: | 29B1 scFv |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | JC polyomavirus major capsid protein VP1 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: T
Mutation: NULL
| >7PAA_T|Chain A[auth KKK], L[auth WWW], M[auth XXX], N[auth YYY], O[auth ZZZ], P[auth aaa], Q[auth bbb], R[auth ccc], S[auth ddd], T[auth eee]|scFv 29B1|Homo sapiens (9606) GSYVLTQPPSVSVAPGKTARITCGGNNIGSRSVHWYQHKPGQAPVMIISYDMNRPSGIPERVSGSNYGNTATLTISRVEAGDEADYYCQVWDSRSDHPYVFGTGTRVTVLGSTSGSGKPGSGEGSTKGEVQLVESGGGLVKPGGSLRLSCAASGITFQYYAMNWVRQAPGKGLEWVSSIGGRGDTTYYTDSVKGRFTISRDNSKSTLYLQMNSLRAEDTAVYYCAKEPFDSSGDHRGVFDYWGQGTLVTVSS |
Antigen
Chain: D
Mutation: NULL
| >7PAA_D|Chain B[auth AAA], C[auth BBB], D[auth CCC], E[auth DDD], F[auth EEE], G[auth FFF], H[auth GGG], I[auth HHH], J[auth III], K[auth JJJ]|Major capsid protein VP1|JC polyomavirus (10632) GSHMGGVEVLEVKTGVDSITEVECFLTPEMGDPDEHLRGFSKSISISDTFESDSPNRDMLPCYSVARIPLPNLNEDLTCGNILMWEAVTLKTEVIGVTSLMNVHSNGQATHDNGAGKPVQGTSFHFFSVGGEALELQGVLFNYRTKYPDGTIFPKNATVQSQVMNTEHKAYLDKNKAYPVECWVPDPTRNENTRYFGTLTGGENVPPVLHITNTATTVLLDEFGVGPLCKGDNLYLSAVDVCGMFTNRSGSQQWRGLSRYFKVQLRKRRVKN |
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)
| T: GLY29 SER30 ARG31 SER32 SER49 TYR50 ASP51 MET52 ASN53 ARG54 PRO55 SER56 ASN66 TRP91 GLU129 GLY154 ILE155 THR156 TYR159 TYR160 PRO228 PHE229 ASP230 SER231 SER232 ASP234 HIS235 ARG236 D: GLU29 GLY31 ASP32 PRO33 ASP34 GLU35 HIS36 ARG38 LYS42 SER45 SER52 SER54 PRO55 ASN56 ARG57 ASP58 LYS146 PRO148 ASP149 GLY150 PHE153 LYS155 LYS176 |
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)
