Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 4854 |
| PDBID: | 7SC1 |
| Chains: | PQ_C |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 3.20 |
| Reference: | 10.1016/j.chom.2021.12.010 |
| Antibody | |
| Antibody: | R40-1G8 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 S 6P spike glycoprotein |
| Antigen mutation: | No |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: P
Mutation: NULL
| >7SC1_P|Chain B[auth H], E[auth M], H[auth P]|R40-1G8 Fab heavy chain|Homo sapiens (9606) EVQLVESGGGLVQPGGSLRLSCAASGLTVSSNYMRWVRQAPGKGLEWVSLIYAGGSTFYADSVKGRFIISRHNSKNILYLQMNSLRAEDTAVYFCARDLYVFGMDVWGQGTAVTVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTH |
Light Chain: Q
Mutation: NULL
| >7SC1_Q|Chain C[auth L], F[auth N], I[auth Q]|R40-1G8 Fab light chain|Homo sapiens (9606) DIQLTQSPSFLSASVGDRVTITCRASQGISSYLAWYQQKPGRAPKLLIYAASTLQSGVPSRFSGSGSGTVFTLTISSLQPEDFATYYCQQLNSDSSTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: C
Mutation: NULL
| >7SC1_C|Chain A, D[auth B], G[auth C]|Spike glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049) MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPASVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPSGRLVPRGSPGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGHHHHHH |
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)
| P: GLU1 VAL2 GLY26 LEU27 THR28 SER30 SER31 ASN32 TYR33 TYR52 ALA53 GLY54 SER56 PHE58 ARG94 ASP95 LEU96 TYR97 VAL98 PHE99 ASP101 Q: ILE2 GLN27 GLY28 ILE29 SER30 TYR32 SER56 SER67 GLY68 THR69 ASN92 SER93 ASP94 C: ARG403 ASP405 GLN409 THR415 GLY416 LYS417 ASP420 TYR421 TYR453 LEU455 PHE456 ARG457 LYS458 SER459 ASN460 GLN474 ALA475 SER477 PHE486 ASN487 TYR489 PHE490 GLN493 SER494 TYR495 GLY496 GLN498 ASN501 VAL503 TYR505 |
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)
