Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 478 |
| PDBID: | 3EZJ |
| Chains: | D_C |
| Organism: | Escherichia coli ETEC H10407, Lama glama |
| Method: | XRD |
| Resolution (Å): | 2.80 |
| Reference: | 10.1016/j.str.2008.11.011 |
| Antibody | |
| Antibody: | NBGSPD_7 Nanobody |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | General secretion pathway protein GspD |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: D
Mutation: NULL
| >3EZJ_D|Chain E[auth B], F[auth D], G[auth F], H|NANOBODY NBGSPD_7|LAMA GLAMA (9844) QVQLQESGGGLVQAGGSLRLSCAASGSIFSINSMDWDRQAPGKQRELVATITSGGSTNYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCNANVKTWAGMTRDYWGQGTQVTVSSHHHHHH |
Antigen
Chain: C
Mutation: NULL
| >3EZJ_C|Chain A, B[auth C], C[auth E], D[auth G]|General secretion pathway protein GspD|Escherichia coli (316401) GAMAEEATFTANFKDTDLKSFIETVGANLNKTIIMGPGVQGAVSIRTMTPLNERQYYQLFLNLLEAQGYAVVPMENDVLKVVKSSAAKVEPLPLVGEGSDNYAGDEMVTKVVPVRNVSVRELAPILRQMIDSAGSGNVVNYDPSNVIMLTGRASVVERLTEVIQRVDHAGNRTEEVIPLDNASASEIARVLESLTKNSGENQPATLKSQIVADERTNSVIVSGDPATRDKMRRLIRRLDSE |
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)
| D: GLN1 ASP35 ASP37 GLN39 LYS43 GLN44 ARG45 GLU46 LEU47 TYR94 ASN96 ASN98 THR101 TRP102 ALA103 GLY104 MET105 THR106 ARG107 ASP108 TYR109 TRP110 GLY111 C: ARG50 GLN51 TYR53 GLN54 LEU57 ASN58 GLU61 VAL67 VAL68 PRO69 ARG116 PRO120 ILE121 ARG123 GLN124 ILE126 ASP127 ASN133 VAL134 VAL135 ASN136 TYR137 ASP138 PRO139 MET144 ARG161 |
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)
