Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5680 |
| PDBID: | 7YKJ |
| Chains: | AD_C |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 3.50 |
| Reference: | 10.1080/22221751.2022.2146538 |
| Antibody | |
| Antibody: | P3E6 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: A
Mutation: NULL
| >7YKJ_A|Chain C[auth A]|P3E6 heavy chain|Homo sapiens (9606) EVQLLDSGGGLVQPGGSLRLSCAVSGFTFSNYAMNWVRQTPGKELEWVSAISGTGDDTHYADSVRGRFTISSDNSKNTVYLQMNSLRVEDTAIYYCAKAISRYPWGCLDYWGQGTLVTVSS |
Light Chain: D
Mutation: NULL
| >7YKJ_D|Chain D|P3E6 light chain|Homo sapiens (9606) EIVLTQSPGTLSLSPGERATLSCRASQSVSNSYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGTSPRLTFGGGTKVEIK |
Antigen
Chain: C
Mutation: A67V/A93I/F140D/206I/G336D/S368L/S370P/S372F/K414N/N437K/G443S/S474N/T475K/E481A/Q490R/G493S/Q495R/N498Y/Y502H/T544K/D611G/H652Y/N676K/P678H/R679G/R680S/R682S/N761K/D793Y/N853K/Q951H/N966K/L978F/K983P/V984P
| >7YKJ_C|Chain A[auth B], B[auth C]|Spike glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049) MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLKGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFKGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDIFSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQ |
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)
| A: THR28 SER30 ASN31 TYR32 THR54 ASP57 HIS59 ILE100 SER101 ARG102 TYR103 PRO104 TRP105 D: SER30 ASN31 TYR33 TYR50 GLY93 THR94 SER95 PRO96 C: ASN343 THR345 ARG346 ASN439 LYS440 LEU441 ASP442 SER443 LYS444 VAL445 SER446 ASN448 ASN450 PRO499 THR500 TYR501 GLY502 VAL503 GLN506 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)
