Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5523 |
| PDBID: | 7X2K |
| Chains: | B_E |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens, Vicugna pacos |
| Method: | XRD |
| Resolution (Å): | 2.40 |
| Reference: | 10.1038/s41467-022-35642-2 |
| Antibody | |
| Antibody: | 70 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
| >7X2K_B|Chain D[auth B]|Nb70|Vicugna pacos (30538) QVQLVESGGGLVQAGGSLRLSCVASGRTFSRYAMGWFRQAPGKEREFVAVIEWDGGTSYYVDSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAAGGNQYYSATYSIWNEYDFWGQGTQVTVSS |
Antigen
Chain: E
Mutation: NULL
| >7X2K_E|Chain A[auth E]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCG |
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: GLN1 THR28 ARG31 TYR32 GLU52 TRP53 ASP54 GLY100 ASN101 GLN102 TYR103 TYR104 ASN112 GLU113 TYR114 ASP115 PHE116 TRP117 E: TYR369 SER371 ALA372 PHE374 SER375 THR376 PHE377 LYS378 CYS379 TYR380 GLY381 VAL382 SER383 PRO384 THR385 ARG408 ALA411 PRO412 GLY413 GLN414 THR415 ASP427 ASP428 PHE429 THR430 |
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)
