Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5560 |
| PDBID: | 7X7D |
| Chains: | B_A |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Vicugna pacos |
| Method: | XRD |
| Resolution (Å): | 2.92 |
| Reference: | 10.3389/fimmu.2022.865401 |
| Antibody | |
| Antibody: | Nb22 Nanobody |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Delta spike glycoprotein RBD |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Chain: B
Mutation: NULL
| >7X7D_B|Chain B, D[auth C], F|Nb22|Vicugna pacos (30538) GPQVQLVESGGNLVQPGGSLRLSCAASGGTLASFAVGWFRQAPGKEREGVSCIDVINRANYADSVKGRFTISRDSAKNTVYLQMNSLEPEDTAVYSCAAHFVPPGSRLRGCLVNELYNYWGQGTQVTVSS |
Antigen
Chain: A
Mutation: L119R/T145K
| >7X7D_A|Chain A, C[auth D], E|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) NLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYRYRLFRKSNLKPFERDISTEIYQAGSKPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGP |
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)
| B: GLY1 PRO2 GLN3 VAL4 GLY28 GLY29 THR30 ALA32 SER33 PHE34 VAL55 ILE56 ASN57 ARG58 ARG73 ASP74 SER75 ALA76 ASN78 PHE101 PRO104 GLY105 ARG107 ASN118 TYR119 A: ARG346 ARG403 LYS417 LYS444 GLY446 GLY447 ASN448 TYR449 ASN450 ARG452 TYR453 LEU455 PHE456 THR470 ILE472 GLU484 GLY485 PHE486 TYR489 PHE490 LEU492 GLN493 SER494 GLY496 GLN498 TYR505 |
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)
