Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 4375 |
| PDBID: | 7MZG |
| Chains: | HL_A |
| Organism: | Homo sapiens, Severe acute respiratory syndrome coronavirus 2 |
| Method: | XRD |
| Resolution (Å): | 2.00 |
| Reference: | 10.1016/j.celrep.2021.109822 |
| Antibody | |
| Antibody: | PDI 42 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
| >7MZG_H|Chain A[auth H]|PDI 42 heavy chain|Homo sapiens (9606) EVQLVESGGGLVQPGGSLRLSCAASGLTVSSNYMSWVRQAPGKGLEWVSVFYPGGSTYNADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARDAVYYGMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC |
Light Chain: L
Mutation: NULL
| >7MZG_L|Chain B[auth L]|PDI 42 light chain|Homo sapiens (9606) DIQMTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFAIYYCQESYSTPGLFTFGPGTKVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: A
Mutation: NULL
| >7MZG_A|Chain C[auth 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 GLY26 LEU27 THR28 SER30 SER31 ASN32 TYR33 TYR52 PRO53 GLY54 SER56 TYR58 ARG97 ASP98 ALA99 VAL100 TYR101 TYR102 ASP105 VAL106 L: ASP1 ILE2 GLN27 SER28 SER30 GLN55 TYR92 SER93 THR94 PRO95 GLY96 PHE98 A: ARG403 ASP405 GLU406 ARG408 GLN409 THR415 GLY416 LYS417 ASP420 TYR421 TYR453 LEU455 PHE456 ARG457 LYS458 SER459 ASN460 TYR473 ALA475 GLY476 SER477 GLU484 PHE486 ASN487 TYR489 PHE490 GLN493 TYR495 GLY496 GLN498 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)
