Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 7318 |
| PDBID: | 7OLZ |
| Chains: | C_A |
| Organism: | Vicugna pacos, Severe acute respiratory syndrome coronavirus 2 |
| Method: | XRD |
| Resolution (Å): | 1.75 |
| Reference: | 10.15252/embj.2021107985 |
| Antibody | |
| Antibody: | Re5D06 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: C
Mutation: NULL
| >7OLZ_C|Chain A[auth C]|Nanobody Re5D06|Vicugna pacos (30538) GSQVQLVESGGGLVQPGGSLRLSCAASGITLDYYAIGWFRQAPGKEREGVSRIRSSDGSTNYADSVKGRFTMSRDNAKNTVYLQMNSLKPEDTAVYYCAYGPLTKYGSSWYWPYEYDYWGQGTQVTVSSTS |
Antigen
Chain: A
Mutation: NULL
| >7OLZ_A|Chain C[auth A]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGP |
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 C: THR28 LEU29 ASP30 TYR31 PHE37 GLY47 VAL48 SER49 ARG50 ARG52 ASN59 TYR60 ALA61 TYR98 PRO100 LEU101 THR102 LYS103 TYR104 TRP108 TYR109 TRP110 PRO111 TYR112 GLU113 ASP115 TYR116 A: TYR351 ARG403 LYS417 VAL445 GLY446 GLY447 TYR449 ASN450 LEU452 TYR453 LEU455 PHE456 ILE468 THR470 ILE472 ALA475 GLU484 GLY485 PHE486 TYR489 PHE490 LEU492 GLN493 SER494 TYR495 GLY496 GLN498 THR500 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)
