Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 3408 |
| PDBID: | 7BEP |
| Chains: | AB_E |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 2.61 |
| Reference: | 10.1016/j.cell.2021.02.032 |
| Antibody | |
| Antibody: | COVOX-384 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Spike glycoprotein RBD |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2; P0DTC2; |
Sequence information
Antibody
Heavy Chain: A
Mutation: NULL
| >7BEP_A|Chain B[auth A], G[auth D]|COVOX-384 heavy chain|Homo sapiens (9606) ILFLVATATGVHSEVQLVESGGGLVKPGESLRLSCAASGFTFSDYYMTWIRQAPGKGLEWVSYIRSSGHTIYYADSVKGRFTISRDNAKNSLYLQMNSLRVEDTAVYYCARGGVLRFLEWPLNAFDIWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK |
Light Chain: B
Mutation: NULL
| >7BEP_B|Chain C[auth B], H[auth F]|COVOX-384 light chain|Homo sapiens (9606) ILFLVATATGVHSDIQLTQSPSSLSASVGDRVTITCRASQGISNYLAWYQQKPGKVPKLLIYAASTLQSGVPSRFSGSGSGTDFTLTISSLQPEDVATYYCQKYNNALGTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: E
Mutation: P204K
| >7BEP_E|Chain A[auth C], F[auth E]|Spike glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049) ETGHHHHHHTNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGKK |
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)
| Chain residues position delta_SASA
: residuesposition A: SER30 TYR50 ARG52 SER54 HIS56 THR57 TYR59 ASN74 LEU102 PHE104 LEU105 GLU106 TRP107 B: LEU-11 PHE-10 VAL-8 SER30 TYR32 ASN92 ASN93 ALA94 LEU95 E: LYS417 TYR449 LEU452 LEU455 PHE456 GLU471 ILE472 ASN481 GLY482 VAL483 GLU484 GLY485 PHE486 TYR489 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)
