Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 7220 |
| PDBID: | 7MFU |
| Chains: | C_A |
| Organism: | Severe acute respiratory syndrome coronavirus 2, synthetic construct |
| Method: | XRD |
| Resolution (Å): | 1.70 |
| Reference: | 10.1016/j.jbc.2021.101202 |
| Antibody | |
| Antibody: | 68 synthetic-Nanobody |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 spike glycoprotein RBD |
| Antigen mutation: | No |
| Durg Target: | P0DTC2; P0DTC2; |
Sequence information
Antibody
Chain: C
Mutation: NULL
| >7MFU_C|Chain C, F|Synthetic nanobody #68 (Sb68)|synthetic construct (32630) SSQVQLVESGGGSVQAGGSLRLSCAASGSISSITYLGWFRQAPGKEREGVAALITVNGHTYYADSVKGRFTVSLDNAKNTVYLQMNSLKPEDTALYYCAAAAWGYAWPLHQDDYWYWGQGTQVTVSA |
Antigen
Chain: A
Mutation: NULL
| >7MFU_A|Chain A, D|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) ITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPK |
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)
| C: THR32 ILE52 VAL54 ASN55 HIS57 TYR59 ALA100 TRP101 GLY102 TYR103 ALA104 TRP105 PRO106 HIS108 ASP110 ASP111 TYR112 A: TYR369 ASN370 SER371 ALA372 PHE374 SER375 THR376 PHE377 LYS378 CYS379 SER383 PRO384 THR385 ASP405 ARG408 VAL503 TYR508 |
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)
