Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 3298 |
| PDBID: | 6Z2M |
| Chains: | D_A |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens, Lama glama |
| Method: | XRD |
| Resolution (Å): | 2.71 |
| Reference: | Not available or To be published |
| Antibody | |
| Antibody: | D4 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
| >6Z2M_D|Chain G[auth D], H[auth F]|nanobody D4|Lama glama (9844) QVQLVESGGGLMQAGGSLRLSCAVSGRTFSTAAMGWFRQAPGKEREFVAAIRWSGGSAYYADSVKGRFTISRDKAKNTVYLQMNSLKYEDTAVYYCARTENVRSLLSDYATWPYDYWGQGTQVTVSS |
Antigen
Chain: A
Mutation: NULL
| >6Z2M_A|Chain A, D[auth E]|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)
| D: ARG27 SER30 ARG52 SER54 GLY55 SER57 GLU100 ASN101 VAL102 ARG103 SER104 LEU105 LEU106 TRP112 PRO113 ASP115 TYR116 A: LYS444 GLY446 TYR449 ASN450 LEU452 LEU455 PHE456 THR470 ILE472 GLY482 VAL483 GLU484 GLY485 TYR489 PHE490 LEU492 GLN493 SER494 |
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)
