Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 4463 |
| PDBID: | 7NKT |
| Chains: | B_A |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Vicugna pacos |
| Method: | XRD |
| Resolution (Å): | 2.30 |
| Reference: | 10.15252/embr.202052325 |
| Antibody | |
| Antibody: | NM1226 Nanobody |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Spike glycoprotein RBD |
| Antigen mutation: | No |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Chain: B
Mutation: NULL
| >7NKT_B|Chain B[auth BBB]|neutralizing nanobody NM1226|Vicugna pacos (30538) QVQLVESGGGSVQPGGSLRLSCLGSGSLDYYAIGWFRQAPGKEREGVSCIASSGDRTIYADSVKGRFTISRDYGKNTVYLQMNSLKPEDTAMYYCAALQGSYYYTGFVANEYDYWGQGAPVTVSSEQKLISEEDLKKKHHHHHH |
Antigen
Chain: A
Mutation: NULL
| >7NKT_A|Chain A[auth AAA]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFHHHHHH |
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 B: TYR30 SER52 LEU98 GLN99 GLY100 SER101 TYR102 TYR103 TYR104 THR105 VAL108 ASN110 GLU111 TYR112 ASP113 TYR114 A: LEU50 TYR51 ASN52 SER53 ALA54 SER55 PHE56 SER57 THR58 PHE59 LYS60 CYS61 VAL64 SER65 PRO66 THR67 GLY86 ASP87 ARG90 ASN119 VAL185 GLY186 TYR190 |
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)
