Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 7285 |
| PDBID: | 7NLL |
| Chains: | C_B |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Vicugna pacos |
| Method: | EM |
| Resolution (Å): | 2.89 |
| Reference: | 10.1038/s41467-021-27610-z |
| Antibody | |
| Antibody: | Fu2 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: C
Mutation: NULL
| >7NLL_C|Chain C[auth A], D[auth C]|Nanobody Fu2|Vicugna pacos (30538) QVQLVESGGGLVQPGGSLRLSCAASGFTLDDYAIGWFRQAPGKEREGVSFITSSDGSTYYVDSVKGRFTISRDNAKNTVYLQMNSLTPEDTAIYYCAVGPSFSYTGSTYYRSELPWDYDYWGQGTQVTVSSGGLPETGGHHHHHH |
Antigen
Chain: B
Mutation: NULL
| >7NLL_B|Chain A[auth B], B[auth D]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNGGLPETGG |
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: GLU44 GLU46 TYR59 ASP62 LYS65 PRO100 THR105 GLY106 SER107 THR108 TYR109 TYR110 ARG111 SER112 GLU113 LEU114 PRO115 TRP116 ASP117 B: TYR369 SER371 ALA372 PHE374 SER375 THR376 PHE377 LYS378 CYS379 TYR380 GLY381 VAL382 SER383 PRO384 GLY404 ASP405 VAL407 ARG408 PRO412 GLY502 VAL503 GLY504 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)
