Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1974 |
| PDBID: | 5Y9F |
| Chains: | VU_F |
| Organism: | human papillomavirus 59, Mus musculus |
| Method: | XRD |
| Resolution (Å): | 3.35 |
| Reference: | 10.1128/mBio.00787-17 |
| Antibody | |
| Antibody: | 28F10 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | human papillomavirus 59 Major capsid protein L1 |
| Antigen mutation: | Yes |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: V
Mutation: NULL
| >5Y9F_V|Chain AA[auth L], CA[auth N], L[auth P], N[auth R], P[auth T], R[auth V], T[auth X], V[auth Z], W[auth b], Y[auth d]|heavy chain of Fab fragment of antibody 28F10|Mus musculus (10090) DVKLVESGGGLVKPGGSLKLSCAASGFPFSDYTMSWIRQTPEKRLEWVASISSGGTYTYYPDTVKGRFTISRDNAKNTLYLQMSSLKSEDTAMFYCTRASPYYDYDEGYMDYWGQGTSVTVSSAKTTAPSVYPLAPVCGGTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPALLQSGLYTLSSSVTVTSNTWPSQTITCNVAHPASSTKVDKKIVPA |
Light Chain: U
Mutation: NULL
| >5Y9F_U|Chain BA[auth K], DA[auth M], K[auth O], M[auth Q], O[auth S], Q[auth U], S[auth W], U[auth Y], X[auth a], Z[auth c]|light chains of Fab fragment of antibody 28F10|Mus musculus (10090) DVVMTQTPLSLPVSLGDQASISCRSSQSLVHSNGNTYLHWYLQKSGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVPFTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC |
Antigen
Chain: F
Mutation: C167S
| >5Y9F_F|Chain A, B, C, D, E, F, G, H, I, J|Major capsid protein L1|Human papillomavirus type 59 (37115) MKVYLPPPSVAKVVSTDEYVTRTSIFYHAGSSRLLTVGHPYFKVPKGGNGRQDVPKVSAYQYRVFRVKLPDPNKFGLPDNTVYDPNSQRLVWACVGVEIGRGQPLGVGLSGHPLYNKLDDTENSHVASAVDTKDTRDNVSVDYKQTQLCIIGCVPAIGEHWTKGTASKPTTVVQGDCPPLELINTPIEDGDMVDTGYGAMDFKLLQDNKSEVPLDICQSICKYPDYLQMSADAYGDSMFFCLRREQVFARHFWNRSGTMGDQLPESLYIKGTDIRANPGSYLYSPSPSGSVVTSDSQLFNKPYWLHKAQGLNNGICWHNQLFLTVVDTTRSTNLSVCASTTSSIPNVYTPTSFKEYARHVEEFDLQFIFQLCKITLTTEVMSYIHNMNTTILEDWNFGVTPPPTASLVDTYRFVQSAAVTCQKDTAPPVKQDPYDKLKFWPVDLKERFSADLDQFPLGRKFLLQLGARPKPTIGPRKRAAPAPTSTPSPKRVKRRKSSRK |
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: SER30 ASP31 THR33 SER52 SER53 GLY54 THR56 TYR57 THR58 TYR59 TYR102 TYR103 ASP104 TYR105 ASP106 U: HIS31 TYR37 SER96 THR97 VAL99 PHE101 F: THR266 MET267 GLY268 GLN270 GLU273 TYR276 ILE277 LYS278 ASP281 ILE282 ARG283 ALA284 ASN285 PRO286 TYR289 |
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)
