Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5322 |
| PDBID: | 7WEB |
| Chains: | GI_D |
| Organism: | Homo sapiens, Severe acute respiratory syndrome coronavirus 2 |
| Method: | EM |
| Resolution (Å): | 3.70 |
| Reference: | 10.1038/s41586-022-04466-x |
| Antibody | |
| Antibody: | XGv347 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Omicron variant spike glycoprotein (stage 3) |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: G
Mutation: NULL
| >7WEB_G|Chain A[auth G], B[auth H]|The heavy chain of Fab XGv347|Homo sapiens (9606) QMQLVQSGPEVKKPGTSVKVSCKASGFTFTDVSSLQWVRQARGQRLEWIGWTVVGTGNTNYAPRFQERVTITTDKSTSTAYMELSSLRSEDTAVYYCAAPFCSETSCSDGFDLWGQGTKVTVS |
Light Chain: I
Mutation: NULL
| >7WEB_I|Chain C[auth I], D[auth L]|The light chain of Fab XGv347|Homo sapiens (9606) EIVLTQSPGTLSLSPGDRATLSCRASQSVRISYLAWYQQKPGQAPRLLISGSSSRATGIPDRFSASGSGTDFTLTISRLEPEDFAVYYCQQYANSPWTFGQGTKVEV |
Antigen
Chain: D
Mutation: A67V/A93I/F140D/G336D/S368L/S370P/S372F/K414N/N437K/G443S/S474N/T475K/E481A/Q490R/G493S/Q495R/N498Y/Y502H/T544K/D611G/H652Y/N676K/P678H/N761K/D793Y/N853K/Q951H/N966K/L978F
| >7WEB_D|Chain E[auth B], F[auth C], G[auth D]|Spike glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049) MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPILVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLKGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFKGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDIFSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT |
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)
| G: ASP31 VAL32 SER34 TRP51 VAL53 GLY55 THR56 GLY57 ASN58 PRO100 GLU104 THR105 SER106 CYS107 SER108 ASP109 GLY110 PHE111 I: SER32 TYR33 GLY51 SER53 SER54 TYR92 ASN94 TRP97 D: ASN414 LEU452 PHE453 TYR470 ALA472 GLY473 ASN474 LYS475 PRO476 CYS477 ALA481 GLY482 PHE483 ASN484 CYS485 TYR486 PHE487 ARG490 |
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)
