Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 3319 |
| PDBID: | 6ZH9 |
| Chains: | D_C |
| Organism: | Homo sapiens, Severe acute respiratory syndrome coronavirus 2, Lama glama |
| Method: | XRD |
| Resolution (Å): | 3.31 |
| Reference: | 10.1038/s41594-020-0469-6 |
| Antibody | |
| Antibody: | H11-H4 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
| >6ZH9_D|Chain D[auth FFF]|Nanobody H11-H4|Lama glama (9844) QVQLVESGGGLMQAGGSLRLSCAVSGRTFSTAAMGWFRQAPGKEREFVAAIRWSGGSAYYADSVKGRFTISRDKAKNTVYLQMNSLKYEDTAVYYCAQTHYVSYLLSDYATWPYDYWGQGTQVTVSSKHHHHHH |
Antigen
Chain: C
Mutation: NULL
| >6ZH9_C|Chain C[auth EEE]|Spike glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049) ITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPK |
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 D: PHE29 ARG52 SER54 GLY55 SER57 ALA58 HIS100 TYR101 VAL102 SER103 TYR104 LEU105 LEU106 TRP112 C: ARG15 LYS113 TYR118 ASN119 LEU121 LEU124 PHE125 THR139 ILE141 GLY151 VAL152 GLU153 TYR158 PHE159 LEU161 GLN162 SER163 |
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)
