Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 3980 |
| PDBID: | 7KN4 |
| Chains: | HL_A |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 2.70 |
| Reference: | 10.1002/advs.202102181 |
| Antibody | |
| Antibody: | S-E6 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
| >7KN4_H|Chain C[auth H], E[auth M]|S-E6 Fab heavy chain|Homo sapiens (9606) QVTLRESGPGLVKPSETLSLTCAVSGGSLSSVNYYWSWIRQHPGKGLEWIGYIYYSGSTNYNPSLKSRVTMSLDTSKNQFSLKLSSVTAADTAVYYCATPGAIMGALHIWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC |
Light Chain: L
Mutation: NULL
| >7KN4_L|Chain D[auth L], F[auth N]|S-E6 Fab light chain|Homo sapiens (9606) QAVLTQPSSASSTPGQRVIISCSGSSSNIGSNTVSWYQQVPGAAPKLLIYFDYRRPSGVPDRFSGTRSGTSASLGISGLQSEDEADYYCAAWDDSLSAWVFGRGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS |
Antigen
Chain: A
Mutation: NULL
| >7KN4_A|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 H: GLN1 VAL32 ASN33 TYR34 PRO95 GLY96 ALA97 ILE98 HIS101 ILE102 L: GLY29 SER30 THR32 TYR49 PHE50 ASP51 TYR52 ARG53 SER56 THR65 ARG66 SER67 GLY68 THR69 SER70 A: ARG403 GLY447 TYR449 TYR453 LEU455 PHE456 TYR473 ALA475 GLY476 SER477 THR478 GLU484 GLY485 PHE486 ASN487 TYR489 PHE490 LEU492 GLN493 SER494 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)
