Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 4379 |
| PDBID: | 7MZJ |
| Chains: | NM_B |
| Organism: | Homo sapiens, Severe acute respiratory syndrome coronavirus 2 |
| Method: | XRD |
| Resolution (Å): | 2.40 |
| Reference: | 10.1016/j.celrep.2021.109822 |
| Antibody | |
| Antibody: | PDI 93 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: N
Mutation: NULL
| >7MZJ_N|Chain H, I[auth N]|PDI 93 heavy chain|Homo sapiens (9606) VVQLVESGGGLVKPGGSLRLSCAASGFTFSYAWMSWVRQAPGKGLEWVGRIKRKSDGGTTDYAAPVKGRFTISRDDSKNTLYLQMSSLKTEDTAVYYCTTDLCRSTSCEHDAFDIWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH |
Light Chain: M
Mutation: NULL
| >7MZJ_M|Chain G[auth L], J[auth M]|PDI 93 light chain|Homo sapiens (9606) DIQMTQSPSSLSASVGDRVTVTCRASQSIRSYLNWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYTTPAITFGQGTRVQIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: B
Mutation: NULL
| >7MZJ_B|Chain C[auth A], F[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 N: SER30 TYR31 TRP33 LYS52 ARG53 LYS54 SER55 ASP56 CYS103 SER105 THR106 CYS108 GLU109 HIS110 ASP111 M: GLN27 ARG30 SER31 TYR32 ALA50 ALA51 SER52 SER91 TYR92 THR93 THR94 PRO95 B: THR345 ARG346 SER349 TYR351 ALA352 ASN440 LEU441 ASP442 SER443 LYS444 VAL445 GLY446 GLY447 ASN448 TYR449 ASN450 LEU452 ARG466 ILE468 THR470 ILE472 GLU484 PHE490 LEU492 GLN493 SER494 PRO499 |
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)
