Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5058 |
| PDBID: | 7TM0 |
| Chains: | IH_A |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 3.10 |
| Reference: | 10.1126/science.abn8652 |
| Antibody | |
| Antibody: | S2L20 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 S B.1.1.529 Omicron variant spike glycoprotein |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2; P0DTC2; |
Sequence information
Antibody
Heavy Chain: I
Mutation: NULL
| >7TM0_I|Chain E, G, I|S2L20 Fab heavy chain|Homo sapiens (9606) EVQLVESGGGVVQPGGSLRLSCAASGFTFNSYGMHWVRQAPGKGLEWVAFIRYDGGNKYYADSVKGRFTISRDNSKNTLYLQMKSLRAEDTAVYYCANLKDSRYSGSYYDYWGQGTLVTVSS |
Light Chain: H
Mutation: NULL
| >7TM0_H|Chain D, F, H|S2L20 Fab light chain|Homo sapiens (9606) VIWMTQSPSSLSASVGDRVTITCQASQDIRFYLNWYQQKPGKAPKLLISDASNMETGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQYDNLPFTFGPGTKVDFK |
Antigen
Chain: A
Mutation: A67V/A93I/F140D/K206I/G336D/S368L/S370P/S372F/K414N/N437K/G443S/S474N/T475K/E481A/Q490R/G493S/Q495R/N498Y/Y502H/T544K/D611G/H652Y/N676K/P678H/R679S/R680G/R682G/Y704C/N761K/D793Y/F814P/N853K/T880C/A889P/A896P/A939P/Q951H/N966K/L978F/V984P
| >7TM0_A|Chain A, B, C|Spike glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049) MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLKGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHSGAGSVASQSIIAYTMSLGAENSVACSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFKGLTVLPPLLTDEMIAQYTSALLAGTICSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDIFSRLDKPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGSGGLNDIFEAQKIEWHEGSGHHHHHHHH |
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: PHE31 ASP50 I: GLU1 GLY15 GLY26 PHE27 THR28 SER31 TYR32 TYR53 ASP54 GLY66 THR69 ASN74 SER75 LYS84 SER85 LYS100 ASP101 SER102 ARG103 TYR104 SER105 GLY106 SER107 TYR108 A: PRO25 PRO26 TYR28 ASN61 THR63 VAL83 PRO85 ASN87 THR108 THR109 LYS113 THR236 ARG237 TYR269 GLN271 PRO272 THR323 GLU324 SER325 THR531 ASN532 |
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)
