Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5683 |
| PDBID: | 7YOW |
| Chains: | BA_C |
| Organism: | Homo sapiens, Severe acute respiratory syndrome coronavirus 2 |
| Method: | XRD |
| Resolution (Å): | 3.30 |
| Reference: | 10.1038/s42003-023-04782-6 |
| Antibody | |
| Antibody: | NCV2SG48 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Omicron spike glycoprotein RBD |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: B
Mutation: NULL
| >7YOW_B|Chain B, E[auth H]|Fab Heavy chain|Homo sapiens (9606) EVQLVESGGGLIQPGGSLRLSCAASGFIVSRNYMNWVRQAPGKGLEWVALIYSGGSTFYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARDLVVYGLDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTGHHHHHH |
Light Chain: A
Mutation: NULL
| >7YOW_A|Chain A, D[auth L]|Fab Light chain|Homo sapiens (9606) AIQLTQSPSSLSASVGDRVTITCRASQGISSHLAWYQQKPGKAPKLLIFAASTLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQHLNSNPPITFGQGTRLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: C
Mutation: G19D/S51L/S53P/S55F/K97N/N120K/G126S/S157N/T158K/E164A/Q173R/G176S/Q178R/N181/Y185H
| >7YOW_C|Chain C, F[auth R]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) QPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNTGHHHHHH |
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)
| A: ILE2 GLN27 GLY28 ILE29 SER30 HIS32 GLN55 SER56 HIS90 ASN92 SER93 ASN94 PRO95 B: VAL2 GLY26 PHE27 ILE28 SER30 ARG31 ASN32 TYR33 TYR52 SER53 GLY54 SER56 PHE58 ARG97 ASP98 LEU99 VAL100 VAL101 TYR102 ASP105 TYR106 C: ARG403 ASP405 GLU406 GLN409 THR415 GLY416 ASN417 ASP420 TYR421 TYR453 LEU455 PHE456 ARG457 LYS458 SER459 ASN460 TYR473 GLN474 ALA475 GLY476 ASN477 LYS478 PHE486 ASN487 TYR489 PHE490 ARG493 TYR495 SER496 ARG498 TYR501 GLY502 HIS505 |
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)
