Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5318 |
| PDBID: | 7WE9 |
| Chains: | IK_F |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 3.60 |
| Reference: | 10.1038/s41586-022-04466-x |
| Antibody | |
| Antibody: | XGv289 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Omicron variant spike glycoprotein |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: I
Mutation: NULL
| >7WE9_I|Chain D[auth C], E[auth H], F[auth I]|The heavy chain of Fab XGv289|Homo sapiens (9606) QVQLVQSGAEVKKPGASLKVSCRASGYTFTSHFIHWVRQAPGQGLEWMGIINPSGGASYAQNFRDRVTMTTDPSTSTVYMELGSLRSEDTAVYYCARAEGSSWLGWFDPWGQGTLVTVSS |
Light Chain: K
Mutation: NULL
| >7WE9_K|Chain G[auth J], H[auth K], I[auth L]|The light chain of Fab XGv289|Homo sapiens (9606) SVLTQPPSASGTPGQRVTIPCSGSSSNIGNNYVYWYQQLPGTAPKLLVYGNNQRPSGVPDRFSVSKSGTSASLAISGLRSEDEADYYCAAWDDGLSGSGWVFGGGTKLTVL |
Antigen
Chain: F
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
| >7WE9_F|Chain A, B, C[auth F]|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)
| I: PHE33 TRP47 ILE50 ASN52 SER54 GLY55 GLY56 ALA57 SER58 TYR59 GLN61 ARG64 SER101 SER102 TRP103 K: ASN31 ASN32 TRP92 ASP94 GLY95 LEU96 SER97 GLY98 SER99 TRP101 F: PHE372 ASN436 LYS437 SER440 LYS441 VAL442 SER443 ARG495 PRO496 THR497 GLY499 VAL500 GLN503 |
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)
