Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 4403 |
| PDBID: | 7N3D |
| Chains: | HL_C |
| Organism: | Homo sapiens, Severe acute respiratory syndrome coronavirus 2 |
| Method: | XRD |
| Resolution (Å): | 1.53 |
| Reference: | 10.1016/j.isci.2024.108976 |
| Antibody | |
| Antibody: | S24-1564 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Spike glycoprotein NTD |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >7N3D_H|Chain A[auth H]|S24-1564 Fab heavy chain|Homo sapiens (9606) QVQLQESGPGLVKPSETLSLTCTVSGGSISSYYWSWIRQPPGKGLEWIGYVYYSGNTKYNPSLKSRVTISVDTSKNQFSLKLGSVTAADTAVYYCARHSRIEVAGTLDFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC |
Light Chain: L
Mutation: NULL
| >7N3D_L|Chain B[auth L]|S24-1564 Fab light chain|Homo sapiens (9606) DIQMTQSPSSLSASVGDRVTITCRASQSIRSYLNWYQQKRGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSTPPTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: C
Mutation: NULL
| >7N3D_C|Chain C|Nucleoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049) SNMNNTASWFTALTQHGKEDLKFPRGQGVPINTNSSPDDQIGYYRRATRRIRGGDGKMKDLSPRWYFYYLGTGPEAGLPYGANKDGIIWVATEGALNTPKDHIGTRNPANNAAIVLQLPQGTTLPKGFYA |
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 H: SER31 TYR33 TYR50 TYR52 ASN56 LYS58 HIS98 ARG100 ILE101 GLU102 VAL103 ALA104 GLY105 THR106 LEU107 L: ARG30 SER31 TYR32 SER91 TYR92 SER93 THR94 C: ARG68 GLY69 PRO80 ASP81 ILE84 LEU113 GLY114 ALA119 GLY120 LEU121 PRO122 TYR123 TRP132 ALA134 THR135 GLU136 GLY137 ALA138 LEU139 ASN140 THR141 PRO142 ASP144 |
2、We defined interacting paratope-epitope residues by a distance cutoff of < 6 Å . Two amino acids are considered as interacting residues if they have at least one atom within a distance of 6 Å from any atom.
Interacting residues (Atom distance based)
