Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 7207 |
| PDBID: | 7ME7 |
| Chains: | A_R |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Lama glama |
| Method: | EM |
| Resolution (Å): | 3.73 |
| Reference: | 10.1038/s41467-021-24963-3 |
| Antibody | |
| Antibody: | 17 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: A
Mutation: NULL
| >7ME7_A|Chain B[auth A]|Nanobody Nb17|Lama glama (9844) HVQLVESGGGLVQAGGSLRLSCAASGSIFSSNAMSWYRQAPGKQRELVASITSGGNADYADSVKGRFTISRDKNTVYPEMSSLKPADTAVYYCHAVGQEASAYAPRAYWGQGTQVTVSS |
Antigen
Chain: R
Mutation: NULL
| >7ME7_R|Chain A[auth R]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCG |
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)
| A: ILE28 PHE29 SER30 SER31 ASN32 ALA33 MET34 SER35 TYR37 SER50 THR52 SER53 GLY54 GLY55 ASN56 ASP58 ASN74 HIS94 ALA95 VAL96 GLY97 GLN98 GLU99 ALA100 SER101 PRO105 ARG106 ALA107 R: ARG346 PHE347 ALA348 SER349 TYR351 ALA352 TRP353 ASN354 ARG355 LYS444 GLY447 TYR449 ASN450 LEU452 ARG466 ILE468 SER469 THR470 ASN481 GLY482 VAL483 GLU484 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)
