Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 4455 |
| PDBID: | 7NGH |
| Chains: | D_B |
| Organism: | Thermococcus kodakarensis KOD1, synthetic construct |
| Method: | EM |
| Resolution (Å): | 3.50 |
| Reference: | 10.1038/s42003-021-02267-y |
| Antibody | |
| Antibody: | 1 synthetic-Nanobody |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | glutamate transporter homologue |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: D
Mutation: NULL
| >7NGH_D|Chain D|Sybody 1|synthetic construct (32630) GSSSQVQLVESGGGLVQAGGSLRLSCAASGFPVDSQFMHWYRQAPGKEREWVAAIESYGDETYYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCRVLVGWGYYGQGTQVTVSAGRAGEQKLISEEDLNSAVDHHHHHH |
Antigen
Chain: B
Mutation: NULL
| >7NGH_B|Chain A, B, C|Proton/glutamate symporter, SDF family|Thermococcus kodakarensis KOD1 (69014) MGKSLLRRYLDYPVLWKILWGLVLGAVFGLIAGHFGYAGAVKTYIKPFGDLFVRLLKMLVMPIVLASLVVGAASISPARLGRVGVKIVVYYLATSAMAVFFGLIVGRLFNVGANVNLGSGTGKAIEAQPPSLVQTLLNIVPTNPFASLAKGEVLPVIFFAIILGIAITYLMNRNEERVRKSAETLLRVFDGLAEAMYLIVGGVMQYAPIGVFALIAYVMAEQGVRVVGPLAKVVGAVYTGLFLQIVITYFILLKVFGIDPIKFIRKAKDAMITAFVTRSSSGTLPVTMRVAEEEMGVDKGIFSFTLPLGATINMDGTALYQGVTVLFVANAIGHPLTLGQQLVVVLTAVLASIGTAGVPGAGAIMLAMVLQSVGLDLTPGSPVALAYAMILGIDAILDMGRTMVNVTGDLAGTVIVAKTEKELDESKWISHHHHHH |
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 D: PHE31 PRO32 SER35 GLN36 PHE37 HIS39 TYR41 GLU50 TRP51 ALA54 SER57 TYR58 GLU61 THR62 TYR63 TYR64 ALA65 ASP66 LYS69 ARG101 LEU103 VAL104 GLY105 TRP106 GLY107 B: HIS34 ALA38 GLY39 LYS42 ASN114 VAL115 ASN116 LEU117 GLY118 ALA220 GLU221 GLN222 VAL224 ARG225 VAL226 VAL227 GLY228 PRO229 LYS232 PRO379 GLY380 SER381 PRO382 ALA384 LEU385 ALA388 MET389 |
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)
