Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1336 |
| PDBID: | 5F97 |
| Chains: | H_D |
| Organism: | Helicobacter pylori, Lama glama |
| Method: | XRD |
| Resolution (Å): | 2.62 |
| Reference: | 10.1016/j.chom.2015.12.004 |
| Antibody | |
| Antibody: | Nb-ER19 Nanobody |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Blood group antigen binding adhesin BabA of Helicobacter pylori strain A730 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: H
Mutation: NULL
| >5F97_H|Chain E, F, G, H|Nanbody Nb-ER19|Lama glama (9844) QVQLQESGGGLVQPGGSLRLSCAASGSIFSGNVMGWYRQAPGKLREWVAAITPQGVPNYADSVKGRFTISRDNAKNMLYLQMSSLKPEDTALYYCNRLPNYRSWGQGTQVTVSSHHHHHH |
Antigen
Chain: D
Mutation: NULL
| >5F97_D|Chain A, B, C, D|Adhesin binding fucosylated histo-blood group antigen,Adhesin,Adhesin binding fucosylated histo-blood group antigen|Helicobacter pylori (210) ASWSHPQFEKSGGGGGLVPRGSGIQDLSDNYENLSKLLTRYSTLNTLIKLSADPSAINAARENLGASAKNLIGDTKNSPAYQAVLLAINAAVGFWNVLGYATQCGGNANGQESTSSTTIFNNEPGYRSTSITCSLNRYKPGYYGPMSIENFKKLNEAYQILQTALNKGLPALKENNGTIKDVTYSYICYGEGNNNCEIKLADGQKLQQNGGSETTTQTIDGKTVSTTISSKVVDSTAADNTYKQSYTEITNALKDVPDSAQALLAQASTLINTINTACPYFSVTNKSGGPQMEPTRGKLCGFTEEISAIQKMITDAQELVNQTSVINEHEQSTPVGGNNGKPFNPFTDASFAQGMLANASAQAKMLNLAHQVGQTINPDNLTGTFKNFVTGFLATCNNKSTAGTSGTQGSPPGTVTTQTFASGCAYVEQTITNLNNSIAHFGTQEQQIQQAENIADTLVNFGSHHHHHH |
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: SER28 SER31 GLY32 ASN33 VAL34 TYR38 GLN40 GLY43 LYS44 LEU45 ARG46 TRP48 ALA51 THR53 PRO54 GLN55 VAL57 ASN59 ASN74 ARG98 LEU99 PRO100 ASN101 ARG103 D: SER44 THR45 THR48 LEU49 LYS51 LEU52 LEU368 ASN369 HIS372 GLN376 ASN379 ASP381 ASN382 GLU430 THR434 ASN437 ASN438 ILE440 ALA441 HIS442 GLY444 THR445 GLU447 GLN448 GLN451 GLN452 GLU454 ASN455 |
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)
