Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1339 |
| PDBID: | 5F9D |
| Chains: | C_A |
| Organism: | Helicobacter pylori, Lama glama |
| Method: | XRD |
| Resolution (Å): | 2.59 |
| 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 P436 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: C
Mutation: NULL
| >5F9D_C|Chain B[auth C]|Nanobody Nb-ER19|Lama glama (9844) QVQLQESGGGLVQPGGSLRLSCAASGSIFSGNVMGWYRQAPGKLREWVAAITPQGVPNYADSVKGRFTISRDNAKNMLYLQMSSLKPEDTALYYCNRLPNYRSWGQGTQVTVSSHHHHHH |
Antigen
Chain: A
Mutation: NULL
| >5F9D_A|Chain A|Adhesin binding fucosylated histo-blood group antigen,Adhesin,Adhesin binding fucosylated histo-blood group antigen|Helicobacter pylori (210) ASWSHPQFEKSGGGGGLVPRGSGIQDLSDNYENLSKLLTRYSTLNTLIKLSADPSAINAARENLGASAKNLIGDTKNSPAYQAVLLAINAAVGFWNVLGYATQCGGNANGQESTSSTTIFNNEPGYRSTSITCSLNRYKPGYYGPMSIENFKKLNEAYQILQTALNKGLPALKENNGTINVEYTYTCSGGGNTNCDPSLFGIGGDGRNGGSVTKTQTIDGKQVNTTISSKVVQPPHSAAYTEITNALNGVPDSAQALLAQASTLINTINTACPYFSVTNKSGGPQMEPTRGKLCGFTEEISAIQKMITDAQELVNQTSVINEHEQSTPVGGNNGKPFNPFTDASFAQGMLANASAQAKMLNLAHQVGQTINPDNLTGTFKNFVTGFLATCNNKSTAGTSGTQGSPPGTVTTQTFASGCAYVEQTITNLNNSIAHFGTQEQQIQQAENIADTLVNFGSHHHHHH |
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)
| Chain residues position delta_SASA
: residuesposition C: SER31 GLY32 ASN33 VAL34 TYR38 GLN40 GLY43 LYS44 LEU45 ARG46 GLU47 TRP48 ALA51 THR53 PRO54 GLN55 VAL57 ASN59 ARG98 LEU99 PRO100 ASN101 ARG103 A: SER44 THR45 THR48 LEU49 LYS51 LEU52 LEU362 ASN363 HIS366 GLN370 ASN373 ASP375 ASN376 THR428 ASN431 ASN432 ILE434 ALA435 HIS436 GLY438 THR439 GLU441 GLN442 GLN445 GLN446 ASN449 |
2、We defined interacting paratope-epitope residues by a distance cutoff of < 6 Å . Two amino acids are considered as interacting residues if they have at least one atom within a distance of 6 Å from any atom.
Interacting residues (Atom distance based)
