Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5621 |
| PDBID: | 7XRP |
| Chains: | B_A |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Camelus dromedarius |
| Method: | EM |
| Resolution (Å): | 3.88 |
| Reference: | 10.1186/s12951-022-01619-y |
| Antibody | |
| Antibody: | C5G2 VHH |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 spike glycoprotein NTD |
| Antigen mutation: | No |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Chain: B
Mutation: NULL
| >7XRP_B|Chain B|C5G2 nanobody|Camelus dromedarius (9838) DVQLVESGGGSVQAGGSLRLSCAASGKFSHLVFLGWFRQAPGKEREGVAAGLGAYESGYYADSVKGRFTVSLDNAENTVYLQMNSLKPEDTALYYCAALVVLSRDNTEFIAHNYWGQGTQVTVSS |
Antigen
Chain: A
Mutation: NULL
| >7XRP_A|Chain A|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) AYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVE |
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)
| B: ARG104 ASP105 ASN106 THR107 A: GLN115 ASN165 CYS166 THR167 PHE168 GLY199 ILE231 GLY232 ILE233 ASN234 |
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)
