Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 4374 |
| PDBID: | 7MZF |
| Chains: | HL_A |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 2.49 |
| Reference: | 10.1016/j.celrep.2021.109822 |
| Antibody | |
| Antibody: | PDI 37 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
| >7MZF_H|Chain B[auth H]|PDI 37 heavy chain|Homo sapiens (9606) EVQLVESGGGLVQPGGSLRLSCAASEFIVSRNYMSWVRQAPGKGLEWVSVIYSGGTTYYADSVKGRFTISRDSSKNTLYLQMNSLRAEDTAVYYCARDRGDYLFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH |
Light Chain: L
Mutation: NULL
| >7MZF_L|Chain C[auth L]|PDI 37 light chain|Homo sapiens (9606) DIQMTQPPSPLFASVGDRVTITCRASQSISSWLAWYQQKPGKAPKLLIYKASSLESGVPSRFSGSGSETEFTLTISSLQPDDFATYYCQQYNSYFPTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: A
Mutation: NULL
| >7MZF_A|Chain A|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: VAL2 GLU26 PHE27 ILE28 SER30 ARG31 ASN32 TYR33 TYR52 SER53 GLY54 THR56 TYR58 ARG94 ARG96 GLY97 ASP98 ASP102 TYR103 L: ILE2 GLN27 SER28 ILE29 SER30 SER31 TRP32 GLU68 TYR91 ASN92 SER93 TYR94 A: ARG403 ASP405 ARG408 GLN409 THR415 GLY416 LYS417 ASP420 TYR421 TYR453 LEU455 PHE456 ARG457 LYS458 SER459 ASN460 TYR473 GLN474 ALA475 GLY476 SER477 THR478 PHE486 ASN487 TYR489 GLN493 SER494 TYR495 GLN498 PRO499 THR500 ASN501 GLY502 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)
