Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 4384 |
| PDBID: | 7MZK |
| Chains: | HL_A |
| Organism: | Homo sapiens, Severe acute respiratory syndrome coronavirus 2 |
| Method: | XRD |
| Resolution (Å): | 2.25 |
| Reference: | 10.1016/j.celrep.2021.109822 |
| Antibody | |
| Antibody: | PDI 96 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Spike glycoprotein RBD |
| Antigen mutation: | No |
| Durg Target: | P0DTC2; P0DTC2; |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >7MZK_H|Chain F[auth H], H[auth N]|PDI 96 heavy chain|Homo sapiens (9606) LVQLVQSGAEVKKPGASVKISCKASGYTFTSYYMHWVRQAPGQGLEWMGIINPSGGGTSYAQKFQGRVTMTRDTSTSTVYMELTSLRSDDTAVYYCAKDRVTIFWGNGMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH |
Light Chain: L
Mutation: NULL
| >7MZK_L|Chain G[auth L], I[auth M]|PDI 96 light chain|Homo sapiens (9606) DIVMTQSPVSLAVSLGERATIKCKSSQSVLYSSNNKNYLGWYQQKPGQPLRLLIYWASTRESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCHQYSTTPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: A
Mutation: NULL
| >7MZK_A|Chain B[auth A], E[auth B]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) NITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPGSHHHHHH |
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 ILE50 ASN52 GLY57 THR58 SER59 THR102 ILE103 PHE104 TRP105 L: TYR31 SER32 SER33 ASN34 TYR38 THR100 A: ASN343 ARG346 SER373 TRP436 ASN437 ASN439 ASN440 LEU441 SER443 LYS444 VAL445 GLY446 GLN498 PRO499 THR500 |
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)
