Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 3101 |
| PDBID: | 6WAR |
| Chains: | D_C |
| Organism: | Middle East respiratory syndrome-related coronavirus, Lama glama |
| Method: | XRD |
| Resolution (Å): | 3.40 |
| Reference: | 10.1016/j.cell.2020.04.031 |
| Antibody | |
| Antibody: | MERS 55 VHH |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Spike glycoprotein RBD |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: D
Mutation: NULL
| >6WAR_D|Chain B, D, F, H, J, L, N, P|nanobody MERS VHH-55|Lama glama (9844) QVQLQESGGGSVQAGGSLRLSCVASGSIFSINAMDWYRQAPGKQRELVAGITSGGSTNYGDFVKGRFTISRDNAKNTVYLQMDSLKPEDTAVYYCAAEVGGWGPPRPDYWGHGTQVTVSSGSLEVLFQ |
Antigen
Chain: C
Mutation: NULL
| >6WAR_C|Chain A, C, E, G, I, K, M, O|Spike protein|Middle East respiratory syndrome-related coronavirus (1335626) EAKPSGSVVEQAEGVECDFSPLLSGTPPQVYNFKRLVFTNCNYNLTKLLSLFSVNDFTCSQISPAAIASNCYSSLILDYFSYPLSMKSDLSVSSAGPISQFNYKQSFSNPTCLILATVPHNLTTITKPLKYSYINKCSRFLSDDRTEVPQLVNANQYSPCVSIVPSTVWEDGDYYRKQLSPLEGGGWLVASGSTVAMTEQLQMGFGITVQYGTDTNSVCPKLEGSLEVLFQ |
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: ASN32 ALA33 ASP35 LEU47 THR52 SER53 GLY54 SER56 THR57 ASN58 TYR59 ASP61 ARG71 ASN73 GLU95 GLY98 TRP99 C: LYS502 SER504 PHE506 ASP510 ARG511 GLU513 ILE529 PRO531 TRP535 GLY538 ASP539 TYR540 TYR541 ARG542 LYS543 GLN544 TRP553 VAL555 ALA556 SER557 |
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)
