Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 4721 |
| PDBID: | 7R7N |
| Chains: | HL_E |
| Organism: | Homo sapiens, Severe acute respiratory syndrome coronavirus 2 |
| Method: | EM |
| Resolution (Å): | 3.95 |
| Reference: | 10.1038/s41586-021-03807-6 |
| Antibody | |
| Antibody: | S2D106 Fv |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Spike glycoprotein |
| Antigen mutation: | No |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >7R7N_H|Chain A[auth H]|S2D106 FAB heavy chain|Homo sapiens (9606) EVQLVQSGAEVKKPGSSVKVSCKASGGPFSSSAISWVRQAPGQGLEWMGGIIPMVGTANYAQKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCARDSRYCSGGSCYSVWFDPWGQGTLVTVSS |
Light Chain: L
Mutation: NULL
| >7R7N_L|Chain C[auth L]|S2D106 FAB light chain|Homo sapiens (9606) DIQLTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPKVLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSTPRTFGQGTKVEMK |
Antigen
Chain: E
Mutation: NULL
| >7R7N_E|Chain B[auth E]|Spike glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049) MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGHHHHHHHHSAWSHPQFEKGGGSGGGGSGGSAWSHPQFEK |
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)
| Chain residues position delta_SASA
: residuesposition H: VAL2 GLY26 GLY27 PRO28 SER31 TRP47 ILE52 MET54 VAL55 ASN59 ARG101 CYS103 SER104 GLY105 GLY106 SER107 CYS108 VAL111 L: SER30 TYR32 SER91 TYR92 SER93 THR94 ARG96 E: TYR351 LYS417 GLY446 GLY447 TYR449 LEU452 LEU455 PHE456 THR470 ILE472 CYS480 ASN481 GLY482 VAL483 GLU484 GLY485 PHE486 TYR489 PHE490 LEU492 GLN493 SER494 |
2、We defined interacting paratope-epitope residues by a distance cutoff of < 6 Å . Two amino acids are considered as interacting residues if they have at least one atom within a distance of 6 Å from any atom.
Interacting residues (Atom distance based)
