Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6153 |
| PDBID: | 8ERR |
| Chains: | IJ_B |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 3.10 |
| Reference: | 10.1126/science.adc9127 |
| Antibody | |
| Antibody: | S2X324 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Omicron BA.1 spike glycoprotein |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: I
Mutation: NULL
| >8ERR_I|Chain D[auth E], F[auth H], H[auth I]|S2X324 heavy chain|Homo sapiens (9606) QITLKESGPTLVKPTQTLTLTCTFSGFSVTTSGVGVGWIRQPPGKALEYLALIYWDDDKRYSTSLKSRLTITKDTSKNQVVLTMTNMDPVDTATYYCARHTIPSIFDYWGQGILVTVSS |
Light Chain: J
Mutation: NULL
| >8ERR_J|Chain E[auth F], G[auth J], I[auth L]|S2X324 light chain|Homo sapiens (9606) QPVLTQPASVSGSPGQSITISCTATSSDVGNYNYVSWYQHHPGKAPKLMIYEVSNRPSGVSNRFSGSKSGNTASLTISGLQAEDEADYYCSSYTSSSLLFGGGTKLTVLG |
Antigen
Chain: B
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/Y704C/N761K/D793Y/F814P/N853K/T880C/A889P/A896P/A939P/Q951H/N966K/L978F/V984P
| >8ERR_B|Chain A, B, C|Spike glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049) MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLKGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHRRARSVASQSIIAYTMSLGAENSVACSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFKGLTVLPPLLTDEMIAQYTSALLAGTICSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDIFSRLDKPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGSGGLNDIFEAQKIEWHEGSGHHHHHHHH |
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: SER32 GLY33 ARG60 ILE102 PRO103 J: ASP29 VAL30 GLY31 ASN32 TYR35 TYR94 THR95 SER96 SER97 SER98 LEU99 B: THR345 ASN439 LYS440 LEU441 SER443 VAL445 SER446 ARG498 PRO499 THR500 TYR501 GLY502 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)
