Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 3652 |
| PDBID: | 7E5Y |
| Chains: | HL_R |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 3.59 |
| Reference: | 10.1038/s41421-021-00295-w |
| Antibody | |
| Antibody: | 2B11 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
| >7E5Y_H|Chain C, F[auth H]|2B11 Fab Heavy chain|Homo sapiens (9606) EVQLVESGGGLVQPGGSLRLSCAASEITVSSNYMNWVRQAPGKGLEWVSVIYSGGTTYYADSVKGRFTISRDNSENTLYLQMNSLRAEDTAVYYCARDLMEVGGMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC |
Light Chain: L
Mutation: NULL
| >7E5Y_L|Chain B, E[auth L]|2B11 Fab Light chain|Homo sapiens (9606) LPVLTQPPSASGTPGQRVTISCSGSSSNVENDNVNWFQQQVPGSTPKLVIYNDRLRPSGVPDRFSGSKSGTSAYLAISGLQSEDEADYYCVAWDASLQSYVFGTGTKVTVLRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: R
Mutation: NULL
| >7E5Y_R|Chain A, D[auth R]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNF |
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)
| L: SER26 SER27 GLU30 ASN31 ASP32 TRP93 ALA95 GLN98 H: VAL2 GLU26 ILE27 THR28 SER30 SER31 ASN32 TYR33 TYR52 SER53 GLY54 GLY55 THR56 THR57 TYR58 ARG97 LEU99 MET100 GLU101 VAL102 ASP106 VAL107 R: ARG403 ASP405 ARG408 GLN409 THR415 GLY416 LYS417 ASP420 TYR421 TYR453 LEU455 PHE456 ARG457 LYS458 SER459 ASN460 TYR473 GLN474 ALA475 GLY476 SER477 PHE486 ASN487 TYR489 PHE490 GLN493 SER494 THR500 ASN501 GLY502 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)
