Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 3479 |
| PDBID: | 7CQD |
| Chains: | IM_B |
| Organism: | Rattus norvegicus, Aquifex aeolicus VF5, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 3.20 |
| Reference: | 10.1107/S2059798321002527 |
| Antibody | |
| Antibody: | NZ-1 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Putative zinc metalloprotease aq_1964,PA14 from Podoplanin |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: I
Mutation: NULL
| >7CQD_I|Chain A[auth H], E[auth I]|Heavy chain of antigen binding fragment, Fab of NZ-1|Rattus norvegicus (10116) EVQLVESGGGLVQPGRSLKLSCAASGFTFSNYGMAWVRQTPTKGLEWIASISAGGDKTYYGDSVKGRFSISRDNAKTTHYLQMDSLRSEDTATYYCAKTSRVYFDYWGQGVMVTVSSAETTAPSVYPLAPGTALKSNSMVTLGCLVKGYFPEPVTVTWNSGALSSGVHTFPAVLQSGLYTLTSSVTVPSSTWSSQAVTCNVAHPASSTKVDKKIVPREC |
Light Chain: M
Mutation: NULL
| >7CQD_M|Chain B[auth L], D[auth M]|Light chain of antigen binding fragment, Fab of NZ-1|Rattus norvegicus (10116) QFVLTQPNSVSTNLGSTVKLSCKRSTGNIGSNYVNWYQQHEGRSPTTMIYRDDKRPDGVPDRFSGSIDRSSNSALLTINNVQTEDEADYFCHSYSSGIVFGGGTKLTVLGQPKSTPTLTVFPPSTEELQGNKATLVCLISDFYPSDVEVAWKANGAPISQGVDTANPTKQGNKYIASSFLRLTAEQWRSRNSFTCQVTHEGNTVEKSLSPAECV |
Antigen
Chain: B
Mutation: NULL
| >7CQD_B|Chain C[auth A], F[auth B]|Putative zinc metalloprotease aq_1964,PA14 from Podoplanin,Putative zinc metalloprotease aq_1964|Aquifex aeolicus VF5 (224324) GSEVPKYLKEPVVVGYVQRDSIAQKIGIKPGDKIIKINGYEVRTWEDLRDALIRLSLDGVKETTLFLERNGEVLHLTIKVPNVQKGEELGIAPLVKPVVGGVKKGSPADQVGIKPGDLILEVNEGGVAMPGAEDDVVGKKINTWYELVEEVRKSQGKAIKLKILRNGKMIEKELIPAKDPKTGTYFIGLFPKTE |
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)
| M: TYR52 ARG70 HIS111 TYR113 SER114 SER115 GLY116 ILE117 I: ASN50 TYR51 GLY52 TRP66 SER69 ILE70 SER71 ALA72 GLY73 ASP75 LYS76 TYR78 THR118 SER119 ARG120 VAL121 TYR122 PHE123 B: VAL235 GLN253 LYS255 |
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)
