Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6525 |
| PDBID: | 7RXD |
| Chains: | N_R |
| Organism: | Escherichia coli, Staphylococcus aureus, Streptococcus sp., Mus musculus, Vicugna pacos, Severe acute respiratory syndrome coronavirus 2 |
| Method: | EM |
| Resolution (Å): | 3.60 |
| Reference: | 10.1073/pnas.2115001118 |
| Antibody | |
| Antibody: | Nb_RBD 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: N
Mutation: NULL
| >7RXD_N|Chain D[auth N]|Nb_RBD|Vicugna pacos (30538) QVQLVESGGGLVQAGGSLRLSCAASGFPVYRDRMAWYRQAPGKEREWVAAIYSAGQQTRYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCNVKDVGHHYEYYDYWGQGTQVTVSSLEHHHHHH |
Antigen
Chain: R
Mutation: NULL
| >7RXD_R|Chain E[auth R]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) GDYKDDDDKGGENLYFQGGSGDSTGSSNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGGGGSGSGHHHHHHHH |
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 N: GLN1 GLY26 PHE27 PRO28 TYR30 ARG31 ASP32 ARG33 TYR37 GLU44 ARG45 GLU46 TRP47 TYR52 SER53 ALA54 GLY55 ARG59 TYR60 ALA61 ASP62 LYS99 ASP100 VAL101 GLY102 HIS103 TYR105 TYR107 R: TYR351 ARG403 ASP405 GLU406 GLN409 LYS417 LYS444 GLY446 GLY447 TYR449 ASN450 LEU452 TYR453 LEU455 PHE456 THR470 GLU471 ILE472 GLY482 VAL483 GLU484 GLY485 PHE486 TYR489 PHE490 LEU492 GLN493 SER494 GLY496 GLN498 ASN501 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)
