Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 7306 |
| PDBID: | 7OAO |
| Chains: | B_A |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Lama glama |
| Method: | XRD |
| Resolution (Å): | 1.50 |
| 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: | No |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Chain: B
Mutation: NULL
| >7OAO_B|Chain B[auth FFF]|C5 nanobody|Lama glama (9844) QVQLVESGGGSVQAGGSLTLSCVASGVTLGRHAIGWFRQAPGKERERVSCIRTFDGITSYVESTKGRFTISSNNAMNTVYLQMNSLKPEDTAVYFCALGVTAACSDNPYFWGQGTQVTVSSKHHHHHH |
Antigen
Chain: A
Mutation: NULL
| >7OAO_A|Chain A[auth EEE]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) PNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNKHHHHHH |
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: GLY26 VAL27 THR28 LEU29 GLY30 ARG31 HIS32 THR53 PHE54 ASP55 GLY56 SER71 SER72 ASN73 ASN74 ALA75 MET76 VAL100 THR101 ALA102 TYR109 PHE110 A: ARG74 GLY117 TYR120 LEU123 TYR124 LEU126 PHE127 GLU155 GLY156 PHE157 TYR160 PHE161 LEU163 GLN164 SER165 TYR166 GLY167 GLN169 ASN172 TYR176 |
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)
