Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6035 |
| PDBID: | 8DT8 |
| Chains: | H_A |
| Organism: | Severe acute respiratory syndrome coronavirus 2, synthetic construct |
| Method: | EM |
| Resolution (Å): | 3.34 |
| Reference: | 10.1073/pnas.2216612120 |
| Antibody | |
| Antibody: | LM18 VHH |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 6P mut7 spike glycoprotein |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2; P0DTC2; |
Sequence information
Antibody
Chain: H
Mutation: NULL
| >8DT8_H|Chain B[auth H]|LM18 nanobody|synthetic construct (32630) EVQLQESGGGLVQPGGSLRLSCAASGFTFSSYALGWYRQAPGKEREWVCAISGSGGSTYYADSVKGRFTCSRDNSKNTLYLQMNSLKPEDTAVYYCARVYQFYGARDYGYPYDFDYWGQGTQVTVSS |
Antigen
Chain: A
Mutation: R682G/R683S/R685S/V705C/F817P/T883C/A892P/A899P/A942P/K986P/V987P
| >8DT8_A|Chain A, D[auth B], E[auth C]|Spike glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049) MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPGSASSVASQSIIAYTMSLGAENSCAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTICSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGSAWSHPQFEKGGGSGGGGSGGSAWSHPQFEK |
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)
| H: GLU44 ARG45 TYR58 TYR96 GLN97 PHE100 TRP103 A: SER373 PHE374 SER375 THR376 LYS378 TYR380 GLY404 ASP405 VAL407 ARG408 GLN414 ASN437 VAL503 GLY504 TYR505 TYR508 |
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)
