Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1319 |
| PDBID: | 5F7N |
| Chains: | C_A |
| Organism: | Helicobacter pylori, Vicugna pacos |
| Method: | XRD |
| Resolution (Å): | 2.28 |
| 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 17875 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: C
Mutation: NULL
| >5F7N_C|Chain C, D|Nanobody Nb-ER19|Vicugna pacos (30538) QVQLQESGGGLVQPGGSLRLSCAASGSIFSGNVMGWYRQAPGKLREWVAAITPQGVPNYADSVKGRFTISRDNAKNMLYLQMSSLKPEDTALYYCNRLPNYRSWGQGTQVTVSSHHHHHH |
Antigen
Chain: A
Mutation: NULL
| >5F7N_A|Chain A, B|Adhesin binding fucosylated histo-blood group antigen|Helicobacter pylori (210) ASWSHPQFEKSGGGGGLVPRGSGIQDLSDNYENLSKLLTRYSTLNTLIKLSADPSAINAARENLGASAKNLIGDTKNSPAYQAVLLAINAAVGFWNVLGYATQCGGNANGQESTSSTTIFNNEPGYRSTSITCSLNRYKPGYYGPMSIENFKKLNEAYQILQTALNKGLPALKENNGTVSVTYTYTCSGEGNDNCSKKATGVSDQNGGTKTKTQTIDGKTVTTTISSKVVDSQAKGNTTRVSYTEITNKLDGVPDSAQALLAQASTLINTINTACPYFSVTNKSGGPQMEPTRGKLCGFTEEISAIQKMITDAQELVNQTSVINEHEQSTPVGGNNGKPFNPFTDASFAQGMLANASAQAKMLNLAHQVGQTINPDNLTGTFKNFVTGFLATCNNKSTAGTSGTQGSPPGTVTTQTFASGCAYVEQTITNLNNSIAHFGTQEQQIQQAENIADTLVNFGSHHHHHH |
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)
| C: SER31 GLY32 ASN33 VAL34 TYR38 GLN40 GLY43 LYS44 LEU45 ARG46 GLU47 TRP48 ALA51 THR53 PRO54 GLN55 VAL57 ASN59 ARG98 LEU99 PRO100 ASN101 A: SER44 THR45 THR48 LEU49 LEU52 LEU365 ASN366 HIS369 GLN373 ASN376 ASP378 ASN379 GLU427 THR431 ASN434 ASN435 ILE437 ALA438 HIS439 GLY441 THR442 GLU444 GLN445 GLN448 GLN449 ASN452 |
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)
