Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5647 |
| PDBID: | 7Y0O |
| Chains: | B_A |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens, Vicugna pacos |
| Method: | EM |
| Resolution (Å): | 4.40 |
| Reference: | Not available or To be published |
| Antibody | |
| Antibody: | P14 VHH |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 spike glycoprotein |
| Antigen mutation: | No |
| Durg Target: | P0DTC2; P0DTC2; |
Sequence information
Antibody
Chain: B
Mutation: NULL
| >7Y0O_B|Chain D[auth B]|P14 nanobody|Vicugna pacos (30538) EEQLVESGGGLVQPGGSLRLSCAASGFRFGSYYMSWVRQAPGKAPEWVSDINTRGETTRYSDSVKGRFTIARDNANNTVFLFMNRLKPEDTAVYYCAVAASGDTFEGRSDPDYWGQGTLVTVS |
Antigen
Chain: A
Mutation: NULL
| >7Y0O_A|Chain A|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) NLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGP |
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: GLN39 GLY42 LYS43 ALA44 PRO45 TYR95 VAL98 ALA99 SER101 THR104 PHE105 GLU106 GLY107 ARG108 SER109 ASP110 PRO111 ASP112 TYR113 TRP114 GLY115 GLN116 A: TYR369 ALA372 PHE374 SER375 THR376 PHE377 LYS378 CYS379 TYR380 GLY381 VAL382 SER383 PRO384 GLY404 ASP405 GLU406 VAL407 ARG408 ASN437 ASN439 ASN440 SER443 PRO499 ASN501 GLY502 VAL503 GLN506 TYR508 |
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)
