Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 4511 |
| PDBID: | 7OAU |
| Chains: | D_C |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Lama glama |
| Method: | XRD |
| Resolution (Å): | 1.65 |
| Reference: | 10.1038/s41467-021-25480-z |
| Antibody | |
| Antibody: | C5 Nanobody |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Spike glycoprotein RBD |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Chain: D
Mutation: NULL
| >7OAU_D|Chain B[auth BBB], D[auth FFF]|C5|Lama glama (9844) MAQVQLVESGGGSVQAGGSLTLSCVASGVTLGRHAIGWFRQAPGKERERVSCIRTFDGITSYVESTKGRFTISSNNAMNTVYLQMNSLKPEDTAVYFCALGVTAACSDNPYFWGQGTQVTVSSHHHHHH |
Antigen
Chain: C
Mutation: N172Y
| >7OAU_C|Chain A[auth AAA], C[auth EEE]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) PNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTYGVGYQPYRVVVLSFELLHAPATVCGPKKSTNKHHHHHH |
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)
| D: GLN3 VAL4 GLY28 VAL29 THR30 LEU31 GLY32 ARG33 HIS34 THR55 PHE56 ASP57 GLY58 SER73 SER74 ASN75 ASN76 ALA77 MET78 VAL102 THR103 ALA104 TYR111 PHE112 C: ARG74 GLY117 TYR120 LEU123 TYR124 LEU126 PHE127 GLU155 GLY156 PHE157 TYR160 PHE161 LEU163 GLN164 SER165 TYR166 GLY167 GLN169 TYR172 TYR176 |
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)
