Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 3817 |
| PDBID: | 7JVB |
| Chains: | C_A |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Lama glama |
| Method: | XRD |
| Resolution (Å): | 3.29 |
| Reference: | 10.1126/science.abe4747 |
| Antibody | |
| Antibody: | Nb20 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: C
Mutation: NULL
| >7JVB_C|Chain B[auth C], D|Nanobody Nb20|Lama glama (9844) QVQLVESGGGLVQAGGSLRLSCAVSGAGAHRVGWFRRAPGKEREFVAAIGASGGMTNYLDSVKGRFTISRDNAKNTIYLQMNSLKPQDTAVYYCAARDIETAEYIYWGQGTQVTVSS |
Antigen
Chain: A
Mutation: NULL
| >7JVB_A|Chain A, C[auth B]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) GRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNF |
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 C: GLY28 ALA29 HIS30 ARG31 PHE35 PHE45 ALA48 ALA51 SER52 MET55 ASN57 TYR58 LEU59 ASP60 ASN72 ARG97 ILE99 GLU100 ALA102 GLU103 TYR104 A: TYR351 LYS417 TYR449 ASN450 LEU452 TYR453 LEU455 PHE456 THR470 ILE472 GLY482 VAL483 GLU484 GLY485 PHE486 TYR489 PHE490 LEU492 GLN493 SER494 GLY496 |
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)
