Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 3979 |
| PDBID: | 7KN3 |
| Chains: | MN_B |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 2.25 |
| Reference: | 10.1002/advs.202102181 |
| Antibody | |
| Antibody: | S-B8 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: M
Mutation: NULL
| >7KN3_M|Chain C[auth H], E[auth M]|S-B8 Fab heavy chain|Homo sapiens (9606) QVQLVQSGGGLIQPGGSLRLSCAASGFTVSLSHMNWVRQAPGKGLEWVSITYGDGNSDYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAREYYYGMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC |
Light Chain: N
Mutation: NULL
| >7KN3_N|Chain D[auth L], F[auth N]|S-B8 Fab light chain|Homo sapiens (9606) DIVMTQSPDSLAVSLGERATINCKSSQSVLYSSNNKNYLAWYQQKPGQPPKLLIYWASTRESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQQYYSLPLTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGECS |
Antigen
Chain: B
Mutation: NULL
| >7KN3_B|Chain A, B|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFSGHHHHHH |
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 M: GLN1 ALA24 SER25 GLY26 PHE27 THR28 LEU31 SER32 HIS33 ILE50 TYR52 GLY53 ASP54 ASN76 ARG94 GLU95 TYR96 TYR97 N: TYR32 TYR91 TYR92 SER93 LEU94 LEU96 B: LYS417 GLY446 TYR449 LEU452 TYR453 LEU455 PHE456 ALA475 GLY476 SER477 VAL483 GLU484 GLY485 PHE486 ASN487 CYS488 TYR489 PHE490 LEU492 GLN493 SER494 TYR495 GLY496 GLN498 ASN501 TYR505 |
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)
