Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5327 |
| PDBID: | 7WEE |
| Chains: | HL_E |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 4.00 |
| Reference: | 10.1038/s41586-022-04466-x |
| Antibody | |
| Antibody: | XGv265 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: H
Mutation: NULL
| >7WEE_H|Chain B[auth H]|The heavy chain of Fab XGv265|Homo sapiens (9606) QITLKESGPTLVKPTQTLTLTCNFSGFSLNTYGVGVGWIRQPPGKALEWLALIYWDGDERYGPFFKNKVTIAKDTSKNQVVLTMTNMDPVDTATYYCARHLIPTIFDYWGQGTLVTVSS |
Light Chain: L
Mutation: NULL
| >7WEE_L|Chain C[auth L]|The light chain of Fab XGv265|Homo sapiens (9606) SALTQPASVSGSPGQSITISCTGTSSDVGGSNYVSWYQHHPDRAPKLLIYEVTNRPSGVSNRFSGSKSANTASLTISGLQAEDEADYYCSSYTTTSTHILFGGGTKLTV |
Antigen
Chain: E
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
| >7WEE_E|Chain A[auth E]|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)
| H: TYR32 GLY33 LEU52 TYR54 TRP55 ASP56 ASP58 ARG60 HIS100 ILE102 PRO103 ILE105 L: SER33 ASN34 TYR35 TYR94 THR95 THR96 THR99 E: THR345 ARG346 ASN439 LYS440 LEU441 ASP442 SER443 LYS444 VAL445 SER446 GLY447 ASN448 TYR449 ASN450 TYR451 ARG498 PRO499 THR500 ARG509 |
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)
