Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 7342 |
| PDBID: | 7PA9 |
| Chains: | VW_J |
| Organism: | JC polyomavirus, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 2.75 |
| Reference: | Not available or To be published |
| Antibody | |
| Antibody: | 98D3 Full-length |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | JC polyomavirus major capsid protein VP1 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: V
Mutation: NULL
| >7PA9_V|Chain BA[auth KKK], CA[auth MMM], K[auth OOO], M[auth QQQ], O[auth TTT], Q[auth VVV], T[auth XXX], V[auth YYY], X[auth bbb], Y[auth ccc]|Fab 98D3 VH|Homo sapiens (9606) EVQLVESGGGVVQPGRSLRLSCAASGFTFSSSAMHWVRQAPGKGLEWVAVISYDGNNQLYADSVKGRLTISRDNSKNALYLQLNSLRTEDTAVYFCARDGGGYSFGTYFFDFWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVL |
Light Chain: W
Mutation: NULL
| >7PA9_W|Chain AA[auth LLL], DA[auth NNN], L[auth PPP], N[auth RRR], P[auth SSS], R[auth UUU], S[auth WWW], U[auth ZZZ], W[auth aaa], Z[auth ddd]|Fab 98D3 VL|Homo sapiens (9606) DIQMTQSPSSLSASVGERVTITCRASQRISNYLNWYQQKPGKAPKLLIYAASTLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSSPPTFGPGTKVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG |
Antigen
Chain: J
Mutation: NULL
| >7PA9_J|Chain A[auth AAA], B[auth BBB], C[auth CCC], D[auth DDD], E[auth EEE], F[auth FFF], G[auth GGG], H[auth HHH], I[auth III], J[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)
| V: SER31 SER52 TYR53 ASN56 ASN57 GLN58 LEU59 GLY101 TYR103 SER104 PHE105 GLY106 THR107 TYR108 W: SER30 ASN31 TYR32 TYR92 J: ASP32 PRO33 ASP34 GLU35 LEU37 LYS42 SER43 SER45 ASN56 ARG57 ASP58 ASN106 GLN108 PRO148 ASP149 PHE245 ASN247 ARG248 SER249 SER251 GLN253 |
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)
