Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6398 |
| PDBID: | 8IDN |
| Chains: | HL_A |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Mus musculus |
| Method: | EM |
| Resolution (Å): | 3.35 |
| Reference: | 10.1107/S2059798323005041 |
| Antibody | |
| Antibody: | E77 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 spike glycoprotein RBD |
| Antigen mutation: | No |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >8IDN_H|Chain B[auth H]|E77 Fab heavy chain|Mus musculus (10090) MGWSCIILFLVATATGVHSQVQLKESGPGLVAPSQSLSITCTVSGLSLIGYGVNWVRQPPGKGLEWLGMIWGDGSTDYNSTLKSRLSISKDNSKSQIFLKMNSLQTIDDARYYCVRDDDYDGQFAYWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC |
Light Chain: L
Mutation: NULL
| >8IDN_L|Chain C[auth L]|E77 Fab light chain|Mus musculus (10090) MGWSCIILFLVATATGVHSQAVVTQESALTTSPGETVTLTCRSSTGAVTISNYVNWVQEKPDHLFTGLIGATNSRAPGVPARFSGSLIGDKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVLGQPKSTPSLTVFPPSSEELKENKATLVCLISNFSPSGVTVAWKANGTPITQGVDTSNPTKEGNKFMASSFLHLTSDQWRSHNSFTCQVTHEGDTVEKSLSPAECL |
Antigen
Chain: A
Mutation: NULL
| >8IDN_A|Chain A|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) ITNLCPFGEVFNATRFATVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTHHHHHH |
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)
| H: ILE49 GLY50 TYR51 TRP71 ASP73 SER75 ASP117 ASP118 ASP119 TYR120 ASP121 GLN123 L: THR49 ILE50 SER51 TYR53 ASN55 ALA71 ASN73 SER74 ARG75 ALA81 SER84 THR97 TRP112 SER114 ASN115 TRP117 A: ARG403 ASP405 GLU406 ARG408 GLN409 GLN414 THR415 GLY416 LYS417 ASP420 TYR421 GLY447 TYR449 TYR453 LEU455 PHE456 TYR473 ALA475 PHE486 ASN487 TYR489 GLN493 SER494 TYR495 GLY496 PHE497 GLN498 THR500 ASN501 GLY502 VAL503 GLY504 TYR505 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)
