Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5693 |
| PDBID: | 7YR1 |
| Chains: | DF_B |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 3.62 |
| Reference: | 10.1016/j.chom.2022.09.018 |
| Antibody | |
| Antibody: | XG2v024 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 BA.2.75 spike glycoprotein |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: D
Mutation: NULL
| >7YR1_D|Chain B[auth D], E, H|XG2v024 Heavy chain|Homo sapiens (9606) VQLVESGGGLVQPGGSLRLSCSASGLTVSSNHMTWVRQAPGKGLEWVSVIYRGGSTYYADSVKGRLTISRDNSKNTLYLQMNSLRAEDTAVYYCARAQGGWELPGAGYYYFYGMDVWGQGTTVTVS |
Light Chain: F
Mutation: NULL
| >7YR1_F|Chain C[auth F], F[auth G], I[auth L]|XG2v024 Light chain|Homo sapiens (9606) IVMTQSPSSLSASVGDRVTITCRASQSISTYLNWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSASGTDFTLTISSLQPEDFATYYCQQSFSTSFTFGPGTKVDI |
Antigen
Chain: B
Mutation: T19I/L24S/P139D/Y144E/N149R/E154L/H207V/I210G/S254S/C336H/L368F/N370P/A372F/S373A/I402N/D405S/Q414N/N437K/S443S/R457K/Q474N/A475K/N481A/Y495R/Q498Y/G502H/L611G/G652Y/T676K/T678H/S680A/R682A/T761K/P793Y/K814P/G889P/I896P/S939P/V951H/L966K/R983P/L984P
| >7YR1_B|Chain A, D[auth B], G[auth C]|Spike glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049) MFVFLVLLPLVSSQCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHENNKSRMESELRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPVNLGRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSSWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFHEVFNATRFASVYAWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSKLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLQSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHRAAASVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT |
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)
| D: PRO14 GLY15 LYS64 GLY65 ARG66 ASN83 SER84 LEU85 ARG86 TRP102 GLU103 LEU104 PRO105 GLY106 ALA107 TYR110 TYR111 F: ILE2 ARG24 SER26 GLN27 SER28 ILE29 SER30 GLY68 THR69 PHE92 B: GLN26 TYR28 SER60 ASN61 VAL62 THR63 PHE65 PRO82 VAL83 LEU84 PRO85 ASN87 THR108 THR109 LEU110 ASP111 LYS113 GLN134 THR236 ARG237 VAL267 GLY268 TYR269 GLN271 THR323 GLU324 THR531 ASN532 VAL534 LYS537 |
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)
