Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 2184 |
| PDBID: | 6EY6 |
| Chains: | I_A |
| Organism: | Porphyromonas gingivalis, Lama glama |
| Method: | XRD |
| Resolution (Å): | 2.10 |
| Reference: | 10.1038/s41467-017-02784-7 |
| Antibody | |
| Antibody: | nb130 Nanobody |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | T9SS component cytoplasmic membrane protein PorM C-terminal part (residues 315-516) |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: I
Mutation: NULL
| >6EY6_I|Chain I, J, K, L, M, N, O, P|nb130|Lama glama (9844) MAQVQLVESGGGLVQAGGSLRLSCAASGRTFSSYVMGWFRQAPGKEREFVTAISWSGGSIHYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYTCVAGFAGYGSFTSRSARDSDKYDYWGQGTKVTVSSHHHHHH |
Antigen
Chain: A
Mutation: NULL
| >6EY6_A|Chain A, B, C, D, E, F, G, H|T9SS component cytoplasmic membrane protein PorM|Porphyromonas gingivalis (837) MGHHHHHHSSGVDLGTENLYFQSVNSITAQVIPQSQIVMSGDTYKANIVLSSVDTTQRPDVFVNGKLLSPENMGLFTATAGAPGTYPVKGYIEMMGNDGVKIRRDFESEYFVTEPMASVAPTMMNVLYAGIDNPINIAVPGVAQQNVSATINNGTLTRRGNLWIARPTKVGSEAIISVTAQSGGRTIQMAKTTLRVRALPDPLPYIEYKDVQGNTKRFKGGRLGKREILAAGGIKAALDDDLLEVNYTVVKFQLVFYDSMGNSIPEVSDGASFSERQKRQIQNLGKGKRFYVTEVIARGPDGIERKIPAIEVIVN |
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)
| I: SER30 SER31 TRP52 SER53 GLY55 SER56 HIS58 ASN73 ALA97 GLY98 TYR99 A: VAL371 GLY372 ALA399 ASP402 VAL451 LYS452 GLN454 VAL468 GLU495 ILE497 GLY503 ILE504 GLU505 ARG506 LYS507 ILE508 PRO509 |
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)
