Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 4488 |
| PDBID: | 7NX7 |
| Chains: | AB_E |
| Organism: | Homo sapiens, Severe acute respiratory syndrome coronavirus 2 |
| Method: | XRD |
| Resolution (Å): | 2.30 |
| Reference: | 10.1016/j.cell.2021.03.055 |
| Antibody | |
| Antibody: | COVOX-222 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Spike glycoprotein RBD |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2; P0DTC2; |
Sequence information
Antibody
Heavy Chain: A
Mutation: NULL
| >7NX7_A|Chain D[auth A]|COVOX-222 Fab heavy chain|Homo sapiens (9606) EVQLVESGGGLIQPGGSLRLSCAASGLTVSSNYMSWVRQAPGKGLEWVSVIYSGGSTFYADSVKGRFTISRDNSKNTLYLQMNSLGAEDTAVYYCARGEGSPGNWFDPWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK |
Light Chain: B
Mutation: NULL
| >7NX7_B|Chain E[auth B]|COVOX-222 Fab light chain|Homo sapiens (9606) DVVMTQSPGTLSLSPGERATLSCRASQSVPSSYLAWYQQKPGQAPRLLIYGASTRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQHYDTSPRFGGGTKVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: E
Mutation: K94N
| >7NX7_E|Chain C[auth E]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) ETGHHHHHHTNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGKK |
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 A: VAL2 GLY26 LEU27 THR28 SER31 ASN32 TYR33 TYR52 SER53 GLY54 SER56 THR57 PHE58 ARG97 SER101 PRO102 GLY103 ASN104 ASP107 PRO108 B: ASP1 VAL2 GLN27 SER28 VAL29 PRO30 SER32 TYR33 HIS91 TYR92 ASP93 THR94 E: ARG403 ASP405 ARG408 THR415 GLY416 ASN417 ASP420 TYR421 TYR449 TYR453 LEU455 PHE456 ARG457 LYS458 SER459 ASN460 TYR473 GLN474 ALA475 GLY476 SER477 PHE486 ASN487 TYR489 GLN493 SER494 TYR495 GLY496 THR500 ASN501 GLY502 VAL503 GLY504 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)
