Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 7217 |
| PDBID: | 7MFU |
| Chains: | B_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: | 14 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: B
Mutation: NULL
| >7MFU_B|Chain B, E|Synthetic Nanobody #14 (Sb14)|synthetic construct (32630) QVQLVESGGGLVQAGGSLRLSCAASGFPVQAREMEWYRQAPGKEREWVAAIKSTGTYTAYAYSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCYVYVGSSYIGQGTQVTVSA |
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)
| Chain residues position delta_SASA
: residuesposition B: ARG32 GLU33 GLU35 TYR37 GLN39 GLU44 ARG45 GLU46 TRP47 ALA50 LYS52 GLY55 THR56 THR58 ALA59 TYR60 ALA61 TYR62 LYS65 TYR95 TYR97 TYR99 GLY101 SER102 SER103 ILE105 GLY106 GLN107 A: ARG403 ASP405 THR415 GLY416 LYS417 ASP420 TYR421 VAL445 GLY446 GLY447 TYR449 LEU452 TYR453 LEU455 PHE456 ASN460 GLU484 PHE486 ASN487 TYR489 PHE490 LEU492 GLN493 SER494 TYR495 GLY496 GLN498 PRO499 THR500 ASN501 GLY502 VAL503 GLY504 TYR505 |
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)
