Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5547 |
| PDBID: | 7X6A |
| Chains: | GJ_D |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 3.50 |
| Reference: | 10.1038/s41586-022-04980-y |
| Antibody | |
| Antibody: | BD55-5840 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Omicron BA.2 spike glycoprotein |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: G
Mutation: NULL
| >7X6A_G|Chain D[auth G], F[auth H], H[auth I]|Heavy chain of Fab BD55-5840|Homo sapiens (9606) VQLAQSGSELRKPGASVKVSCDTSGHSFTSNAIHWVRQAPGQGLEWMGWINTDTGTPTYAQGFTGRFVFSLDTSARTAYLQISSLKADDTAVFYCARERDYSDYFFDYWGQGTLVTVSS |
Light Chain: J
Mutation: NULL
| >7X6A_J|Chain E[auth J], G[auth K], I[auth L]|Light chain of Fab BD55-5840|Homo sapiens (9606) EVVMTQSPASLSVSPGERATLSCRARASLGISTDLAWYQQRPGQAPRLLIYGASTRATGIPARFSGSGSGTEFTLTISSLQSEDSAVYYCQQYSNWPLTFGGGTKVEIK |
Antigen
Chain: D
Mutation: T19I/L24S/P139D/I210G/C336D/L368F/N370P/A372F/S373A/I402N/D405S/Q414N/N437K/Q474N/A475K/N481A/F490R/Y495R/Q498Y/G502H/L611G/G652Y/T676K/T678H/S680A/R682A/T761K/P793Y/K814P/G889P/I896P/S939P/V951H/L966K/R983P/L984P
| >7X6A_D|Chain A, B, C[auth D]|Spike glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049) MFVFLVLLPLVSSQCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHRAAASVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT |
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)
| G: ASN52 THR55 THR57 TYR102 SER103 TYR105 J: GLU1 VAL2 ALA27 SER28 LEU29 GLY30 ASP34 TYR93 SER94 ASN95 TRP96 PRO97 D: PRO337 ASP339 GLU340 VAL341 ASN343 ALA344 THR345 ARG346 LYS356 ARG357 ILE358 LYS440 LEU441 SER443 LYS444 ASN448 ASN450 |
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)
