Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6409 |
| PDBID: | 8IVA |
| Chains: | CE_G |
| Organism: | Homo sapiens, Severe acute respiratory syndrome coronavirus 2, Mus musculus |
| Method: | EM |
| Resolution (Å): | 3.95 |
| Reference: | 10.1093/procel/pwad040 |
| Antibody | |
| Antibody: | XMA01 Fv |
| 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: C
Mutation: NULL
| >8IVA_C|Chain A[auth C]|heavy chain of XMA01|Homo sapiens (9606) EVQLVESGGGLVQPGGSLRLSCSASGFTFSSYAMHWVRQAPGKGLEYVSSISSNGGSTYYADSVKGRFTISRDNSKNTLYLQMSSLRVEDAAVYYCVKHYQQQLLWGGPDVWGQGTTVTVSS |
Light Chain: E
Mutation: NULL
| >8IVA_E|Chain B[auth E]|light chain of XMA01|Homo sapiens (9606) DIQMTQSPVSLSASVGDRVTITCRASQSISTWLAWYQQKPGKAPKLLIYETSSLESGVPSRFSGSGSGTEFTLTISSLQPDDFATYYCQQFNSYPWTFGQGTKVEIK |
Antigen
Chain: G
Mutation: NULL
| >8IVA_G|Chain C[auth G]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) ESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGP |
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)
| C: SER50 ILE51 SER52 SER57 THR58 TYR59 LEU104 LEU105 TRP106 E: ASP1 GLN27 TRP32 ASN92 SER93 TYR94 PRO95 G: LEU455 PHE456 TYR473 ALA475 GLY476 SER477 THR478 GLU484 GLY485 PHE486 ASN487 TYR489 PHE490 LEU492 GLN493 |
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)
