Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 4420 |
| PDBID: | 7N9A |
| Chains: | A_E |
| Organism: | Lama glama, Severe acute respiratory syndrome coronavirus 2 |
| Method: | EM |
| Resolution (Å): | 3.50 |
| Reference: | Not available or To be published |
| Antibody | |
| Antibody: | Nb21 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: A
Mutation: NULL
| >7N9A_A|Chain A|Nanobody Nb21|Lama glama (9844) QVQLVESGGGLVQAGGSLRLSCAVSGLGAHRVGWFRRAPGKEREFVAAIGANGGNTNYLDSVKGRFTISRDNAKNTIYLQMNSLKPQDTAVYYCAARDIETAEYTYWGQGTQVTVSS |
Antigen
Chain: E
Mutation: NULL
| >7N9A_E|Chain B[auth E]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) NLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPK |
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 A: LEU27 GLY28 ALA29 HIS30 ARG31 PHE35 GLU44 PHE45 GLY50 ALA51 ASN52 GLY53 ASN55 ASN57 TYR58 LEU59 ASN72 ARG97 ASP98 ILE99 GLU100 THR101 ALA102 GLU103 TYR104 E: GLY446 GLY447 TYR449 ASN450 LEU452 LEU455 PHE456 THR470 ILE472 GLY482 VAL483 GLU484 GLY485 PHE486 ASN487 CYS488 TYR489 PHE490 LEU492 GLN493 SER494 GLY496 GLN498 |
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)
