Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5469 |
| PDBID: | 7WTF |
| Chains: | IK_D |
| Organism: | Homo sapiens, Severe acute respiratory syndrome coronavirus 2 |
| Method: | EM |
| Resolution (Å): | 3.00 |
| Reference: | 10.1038/s41422-022-00677-z |
| Antibody | |
| Antibody: | XGv051 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Omicron spike glycoprotein |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: I
Mutation: NULL
| >7WTF_I|Chain A[auth G], F[auth H], H[auth I]|Heavy chain of XGv051|Homo sapiens (9606) VQLVQSGAEVKKPGSSVKVSCKASGGTFSNYALSWVRQAPGQGLEWMGGIIPIFGTTNYAQKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCARLDGYSFGHDRYYQDGMDDWGPGT |
Light Chain: K
Mutation: NULL
| >7WTF_K|Chain B[auth J], G[auth K], I[auth L]|Light chain of XGv051|Homo sapiens (9606) DIQMTQSPSSLSASVGDRVTITCRASQAIRNDLGWYQQKPGKAPKCLIYAASSLQSGVPSRFSGSGSGTEFTLTISSLQPEDFATYFCLQQNIYPRTFGQGTKV |
Antigen
Chain: D
Mutation: A54V/A80I/F127D/193I/G323D/S355L/S357P/S359F/K401N/N424K/G430S/S461N/T462K/E468A/Q477R/G480S/Q482R/N485Y/Y489H/T531K/D598G/H639Y/R667A/R669A/N748K/D780Y/F801P/N840K/A876P/A883P/A926P/Q938H/N953K/L965F/K970P/V971P
| >7WTF_D|Chain C[auth B], D[auth C], E[auth D]|Spike glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049) QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLKGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTNSPRAAASVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFKGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDIFSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPRRA |
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)
| I: ASN31 ALA33 TRP47 GLY50 ILE52 PHE55 THR57 ASN59 GLY101 TYR102 SER103 PHE104 HIS106 ASP107 ARG108 TYR109 TYR110 K: GLN27 ARG30 ASN31 SER52 SER53 SER56 ASN92 ILE93 TYR94 D: ARG405 ARG410 GLN411 THR417 GLY418 ASN419 TYR423 TYR451 TYR455 LEU457 PHE458 ALA477 GLY478 ASN479 VAL485 ALA486 GLY487 PHE488 ASN489 TYR491 PHE492 LEU494 ARG495 SER496 SER498 ARG500 TYR503 HIS507 |
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)
