Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 3589 |
| PDBID: | 7DEO |
| Chains: | C_D |
| Organism: | Homo sapiens, Severe acute respiratory syndrome coronavirus 2 |
| Method: | XRD |
| Resolution (Å): | 2.50 |
| Reference: | 10.1371/journal.pbio.3001209 |
| Antibody | |
| Antibody: | PR1077 scFv |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Spike glycoprotein RBD |
| Antigen mutation: | No |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Chain: C
Mutation: NULL
| >7DEO_C|Chain A, C|antibody scFv|Homo sapiens (9606) GSEVQLVESGGGVVQPGRSLRLSCAASGFTFSYYGMHWVRQAPGKGLEWVAVIWYDGSNRFYADSVKGRFTISRDNSKSTLYLQMNSLRAEDTAVYYCATDPPGLRFRFDYWGQGTLVTVSSGGGGSGGGGSGGGGSDIVMTQSPLSLPVTPGEPASISCRSSQSLLHSNGYNYLDWYLQKPGQSPQLLIYLGSNRASGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCMQGLQTPLTFGGGTKVEIKGGGSHHHHHH |
Antigen
Chain: D
Mutation: NULL
| >7DEO_D|Chain B, D|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) NLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSAAAHHHHHH |
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)
| C: GLY-1 VAL2 GLY26 PHE27 THR28 TYR31 TYR32 TRP52 TYR53 ASP54 GLY55 SER56 ASN57 ARG58 PHE59 PRO100 PRO101 GLY102 LEU103 ARG104 PHE105 ARG106 TYR109 HIS166 ASN168 TYR170 TYR189 SER196 LEU232 GLN233 THR234 D: ARG403 LYS417 GLY446 GLY447 TYR449 ASN450 LEU452 TYR453 LEU455 PHE456 THR470 ALA475 VAL483 GLU484 GLY485 PHE486 ASN487 TYR489 PHE490 LEU492 GLN493 SER494 TYR495 GLY496 GLN498 ASN501 TYR505 |
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)
