Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6373 |
| PDBID: | 8HES |
| Chains: | HL_C |
| Organism: | Homo sapiens, Severe acute respiratory syndrome coronavirus 2 |
| Method: | XRD |
| Resolution (Å): | 2.20 |
| Reference: | 10.1038/s41467-023-39890-8 |
| Antibody | |
| Antibody: | NIV-10 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
| >8HES_H|Chain A[auth H]|NIV-10 Fab H-chain|Homo sapiens (9606) EVQLVESGGGLVQPGGSLRLSCAASGFTFYSYWMTWVRQAPGKGLEWVANIKHDESESHYVDSVRGRFTISRDNAKNSVYLQMKGLRAEDTAVYYCARDGGYNILTAYYHAPSYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKGSSLEVLFQGPLGHHHHHH |
Light Chain: L
Mutation: NULL
| >8HES_L|Chain C[auth L]|NIV-10 Fab L-chain|Homo sapiens (9606) QSALTQPASVSGSPGQSITISCTGTSSDVGGYNFVSWYRQYPGKAPQLMIYDVSRRPSGDSDRFSGSKSGNTASLTISGLQAEDEAEYHCSSYTGRSPYVVFGGGTKVTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS |
Antigen
Chain: C
Mutation: NULL
| >8HES_C|Chain B[auth C]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) PTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKN |
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: THR28 TYR30 SER31 TYR32 TRP33 LYS52 HIS53 ASP54 GLU55 SER56 ASN74 ARG98 ASP99 TYR102 ASN103 ILE104 LEU105 THR106 TYR108 HIS110 SER113 TYR114 L: LEU46 TYR49 ARG53 PRO55 SER56 C: ARG403 GLY416 LYS417 ASP420 TYR421 TYR449 LEU452 TYR453 LEU455 PHE456 ARG457 TYR473 ALA475 THR478 VAL483 GLU484 GLY485 PHE486 ASN487 CYS488 TYR489 PHE490 LEU492 GLN493 SER494 GLY496 TYR505 |
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)
