Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 4453 |
| PDBID: | 7NEG |
| Chains: | HL_E |
| Organism: | Homo sapiens, Severe acute respiratory syndrome coronavirus 2 |
| Method: | XRD |
| Resolution (Å): | 2.19 |
| Reference: | 10.1016/j.cell.2021.02.033 |
| Antibody | |
| Antibody: | COVOX-269 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
| >7NEG_H|Chain A[auth H]|Antibody COVOX-269 Fab heavy chain|Homo sapiens (9606) QVQLVESGGGLIQPGGSLRLSCAASGLTVNRNYMSWIRQAPGKGLEWVSVIYSGGSTFYADSVKGRFTISRDNSKNTLSLQMNSLRAEDTAIYYCARDFYEGSFDIWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK |
Light Chain: L
Mutation: NULL
| >7NEG_L|Chain B[auth L]|Antibody COVOX-269 Fab light chain|Homo sapiens (9606) AIQLTQSPSFLSASIGDRVTITCRASQGISSYLAWYQQKPGKAPKLLIYAASTLQSGVPSRFSGSGSGTEFTLTISSLQPEDFASYYCQQLNSYPAPVFGPGTKVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: E
Mutation: NULL
| >7NEG_E|Chain C[auth E]|Surface glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049) MGCVAETGHHHHHHTNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTYGVGYQPYRVVVLSFELLHAPATVCGKK |
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: VAL2 GLY26 LEU27 THR28 ASN30 ARG31 ASN32 TYR33 TYR52 SER53 GLY54 SER56 PHE58 ARG71 ARG97 ASP98 PHE99 TYR100 GLU101 ASP105 ILE106 L: ILE2 GLN27 GLY28 ILE29 SER30 TYR32 SER67 GLN90 LEU91 ASN92 TYR94 E: ARG403 THR415 GLY416 LYS417 ASP420 TYR421 TYR453 LEU455 PHE456 ARG457 LYS458 SER459 ASN460 TYR473 GLN474 ALA475 GLY476 SER477 PHE486 ASN487 TYR489 GLN493 SER494 TYR495 GLN498 THR500 TYR501 GLY502 VAL503 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)
