Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6140 |
| PDBID: | 8ELP |
| Chains: | B_A |
| Organism: | Severe acute respiratory syndrome coronavirus 2, synthetic construct, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 2.83 |
| Reference: | 10.1073/pnas.2216612120 |
| Antibody | |
| Antibody: | Nb-C4-240 VHH |
| 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
| >8ELP_B|Chain B|Nanobody Nb-C4-240|synthetic construct (32630) EVQLQESGGGLVQPGGSLRLSCAASGFTFSSYAMGWYRQAPGKEREWVCAISGSGGSTYYADSVKGRFTCSRDNSKNTLYLQMNSLKPEDTAVYYCARVVSYYDQTGFVYWQSYDYWGQGTQVTVSSGSGHHHHHHHHHH |
Antigen
Chain: A
Mutation: NULL
| >8ELP_A|Chain A|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSGHHHHHH |
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: TYR32 VAL96 SER97 TYR98 TYR99 TYR100 ASP101 A: TYR369 SER371 PHE374 PHE377 LYS378 CYS379 TYR380 GLY381 VAL382 SER383 PRO384 THR385 LYS386 ARG408 ALA411 PRO412 GLY413 GLN414 ASP427 |
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)
