Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 3288 |
| PDBID: | 6YZ7 |
| Chains: | D_A |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens, Lama glama |
| Method: | XRD |
| Resolution (Å): | 3.30 |
| Reference: | Not available or To be published |
| Antibody | |
| Antibody: | 6YZ7 Nanobody |
| 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: D
Mutation: NULL
| >6YZ7_D|Chain D[auth DDD], F[auth FFF]|Nanobody|Lama glama (9844) QVQLVESGGGLMQAGGSLRLSCAVSGRTFSTAAMGWFRQAPGKEREFVAAIRWSGGSAYYADSVKGRFTISRDKAKNTVYLQMNSLKYEDTAVYYCARTENVRSLLSDYATWPYDYWGQGTQVTVSSKHHHHHH |
Antigen
Chain: A
Mutation: NULL
| >6YZ7_A|Chain A[auth AAA], E[auth EEE]|Spike glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049) PNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNKHHHHHH |
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)
| D: PHE29 SER30 ARG52 SER54 GLY55 SER57 ALA58 THR99 GLU100 ASN101 VAL102 ARG103 SER104 LEU105 LEU106 TRP112 PRO113 ASP115 A: ARG17 LYS115 GLY117 TYR120 ASN121 LEU123 LEU126 PHE127 THR141 ILE143 GLY153 VAL154 GLU155 GLY156 TYR160 PHE161 LEU163 GLN164 SER165 |
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)
