Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5309 |
| PDBID: | 7WD1 |
| Chains: | C_B |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Vicugna pacos |
| Method: | XRD |
| Resolution (Å): | 2.50 |
| Reference: | 10.1016/j.xcrm.2023.100918 |
| Antibody | |
| Antibody: | R14 VHH |
| 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
| >7WD1_C|Chain C, D|R14|Vicugna pacos (30538) QVQLQESGGGLVQPGGSLRLSCAVSGFTLDYYAIGWFRQAPGKEREGVSCISSSDGSTSYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTALYYCAATPATYYSGRYYYQCPAGGMDYWGQGTQVTVSS |
Antigen
Chain: B
Mutation: NULL
| >7WD1_B|Chain A, B|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPK |
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: VAL2 THR28 LEU29 ASP30 TYR31 GLY47 VAL48 SER49 CYS50 SER59 TYR60 ALA61 ASP62 THR99 PRO100 ALA101 THR102 TYR103 TYR104 ARG107 TYR108 TYR109 GLN111 CYS112 PRO113 ALA114 GLY115 GLY116 ASP118 TYR119 B: TYR351 ARG403 LYS417 LYS444 VAL445 GLY446 GLY447 TYR449 ASN450 LEU452 TYR453 LEU455 PHE456 ILE468 THR470 ILE472 THR478 GLU484 GLY485 PHE486 ASN487 TYR489 PHE490 LEU492 GLN493 SER494 TYR495 GLY496 GLN498 THR500 ASN501 TYR505 |
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)
