Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6397 |
| PDBID: | 8I5I |
| Chains: | HL_R |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 3.06 |
| Reference: | 10.1038/s42003-023-04782-6 |
| Antibody | |
| Antibody: | NCV2SG53 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Delta spike glycoprotein RBD |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >8I5I_H|Chain B[auth H]|Fab Heavy chain|Homo sapiens (9606) QVQMVESGGGLVRPGGSLRLSCAASGFTFSDYYMSWIRQAPGKGLEWISYISSSGSSMNYADSVKGRFTISRDNAKNSLFLQMNSLRAEDTAVYYCAREFDLTKIIMVPPYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK |
Light Chain: L
Mutation: NULL
| >8I5I_L|Chain C[auth L]|Fab Light chain|Homo sapiens (9606) AIQLTQSPSSLSASVGDRVTITCRASQGISSYLAWYQQKPGKAPKVLIYAASTLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQLKSYPLTFGGGTKVEITRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: R
Mutation: L132R/T158K
| >8I5I_R|Chain A[auth R]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) QPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYRYRLFRKSNLKPFERDISTEIYQAGSKPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNTGHHHHHH |
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: TYR33 TYR50 SER53 SER54 GLY55 SER56 SER57 ARG72 ASP73 ASN74 ALA75 LYS76 PHE100 ASP101 LEU102 LYS104 ILE105 ILE106 MET107 L: GLY28 SER30 TYR32 LEU91 LYS92 SER93 TYR94 PRO95 R: GLY446 TYR449 ARG452 LEU455 PHE456 ALA475 GLY476 SER477 LYS478 PRO479 ASN481 VAL483 GLU484 GLY485 PHE486 ASN487 CYS488 TYR489 PHE490 LEU492 GLN493 SER494 GLY496 GLN498 THR500 ASN501 |
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)
