Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 7103 |
| PDBID: | 5EUL |
| Chains: | V_Y |
| Organism: | Bacillus subtilis subsp. subtilis str. 168, synthetic construct, Geobacillus thermodenitrificans NG80-2, Vicugna pacos |
| Method: | XRD |
| Resolution (Å): | 3.70 |
| Reference: | 10.1038/nature17163 |
| Antibody | |
| Antibody: | AYC08 Nanobody |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Protein translocase subunit SecY |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: V
Mutation: NULL
| >5EUL_V|Chain D[auth V]|AYC08|Vicugna pacos (30538) QVQLVETGGGLVQPGGSLRLSCGASGSIFNMYAMGWYRQAPGKQREVVARIATDDSTMYPDSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCYYQRTVMSQPYWGQGTQVTVSSGGLPETGGHHHHHH |
Antigen
Chain: Y
Mutation: NULL
| >5EUL_Y|Chain B[auth Y]|Protein translocase subunit SecY|Geobacillus thermodenitrificans (strain NG80-2) (420246) MFRTISNFMRVSDIRNKIIFTLLMLIVFRIGTFIPVPSVNTDVLKLQDQLNAFGVLNIFCGGALQNFSIFAMGVMPYITASIIVQLLQMDVVPKFAEWSKQGEMGRRKLAQFTRYFTIVLGFIQALGMSYGFNNLAGGMLIQNPGIGTYLLIAVVLTAGTAFLMWLGEQITAKGVGNGISIIIFAGIVSGIPTILNQIYAQTFGGLNIVRLLLVALAVVAVIVGVIYIQQAFRKIPIQYAKRLEGRNPVGGHSTHLPLKVNPAGVIPVIFAVSFLIAPPTIASFFGTNDVTLWIRRTFDYTHPVGMTIYVVLIIAFTYFYAFVQVNPEQMADNLKKQGGYIPGIRPGKNTQEYVTRILYRLTLVGSLFLAFIAVLPVFFVNFANLPPSAQIGGTSLLIVVGVALETMKQLESQLVKRHYRGFIK |
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)
| V: TYR37 GLN44 ARG45 GLU46 VAL47 ARG50 MET58 TYR59 PRO60 ASP61 TYR96 GLN98 THR100 VAL101 SER103 GLN104 PRO105 Y: PRO35 VAL39 ASN40 THR41 ASP42 VAL43 LYS45 LEU46 GLN47 ASP48 GLN49 VAL55 CYS60 LEU135 GLY137 GLY138 MET139 LEU140 ILE141 GLN142 PRO144 |
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)
