Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 2183 |
| PDBID: | 6EY0 |
| Chains: | H_D |
| Organism: | Porphyromonas gingivalis, Lama glama |
| Method: | XRD |
| Resolution (Å): | 2.40 |
| Reference: | 10.1038/s41467-017-02784-7 |
| Antibody | |
| Antibody: | nb01 Nanobody |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | T9SS component cytoplasmic membrane protein PorM N-terminal part (residues 30-212) |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: H
Mutation: NULL
| >6EY0_H|Chain E, G, H|llama nanobody nb01|Lama glama (9844) MADVQLVESGGGLVQAGGSLRVSCAASGRTFSSYSMGWFRQAPGKEREFVAAISRSDNSTYYADSVKGRFTISRDSAKNTVYLQMNSLKPEDTAVYYCAATPYGSRYYLRELREYDYWGQGTQVTVSSHHHHHH |
Antigen
Chain: D
Mutation: NULL
| >6EY0_D|Chain A, B, C, D|T9SS component cytoplasmic membrane protein PorM|Porphyromonas gingivalis (837) MGHHHHHHSSGVDLGTENLYFQSSLTSSIDGSDKRNNLVLSELNTAYRTNPEKVKVWYERSLVLQKEADSLCTFIDDLKLAIARESDGKDAKVNDIRRKDNLDASSVVMLNPINGKGSTLRKEVDKFRELVATLMTDKAKLKLIEQALNTESGTKGKSWESSLFENMPTVAAITLLTKLQSDVRYAQGEVLADLVKS |
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)
| H: TYR32 ARG52 SER53 ASP54 PRO96 TYR97 GLY98 SER99 ASP101 TYR102 D: GLU87 ASP89 SER90 THR93 PHE94 ASP96 ASP97 LEU98 LEU100 ALA101 ARG104 LYS109 VAL128 ASN134 LYS136 THR139 GLU143 |
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)
