Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5078 |
| PDBID: | 7TPR |
| Chains: | E_C |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Camelus dromedarius |
| Method: | EM |
| Resolution (Å): | 2.39 |
| Reference: | 10.1101/2021.10.27.465996 |
| Antibody | |
| Antibody: | 8A2 VHH |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 variant spike glycoprotein |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2; P0DTC2; |
Sequence information
Antibody
Chain: E
Mutation: NULL
| >7TPR_E|Chain D, E|Nanobody 8A2|Camelus dromedarius (9838) AVQLVDSGGGSVQAGGSLRLSCAASGYTYSICTMGWYRQAPGEGLEWVSGINADGSNTHYTDSVKGRFTISRDNAKKTLYLQMNSLKPEDTAIYYCAAHGTYDKYAPCGGFAGTYTYWGQGTQVTVSSSGQA |
Antigen
Chain: C
Mutation: R668G/R669S/R671S/F803P/A878P/A885P/A928P/K972P/V973P
| >7TPR_C|Chain A, B, C|Spike glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049) CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNH |
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)
| E: ALA1 VAL2 GLN3 LEU4 THR33 TYR37 GLN39 PRO41 GLY42 GLU43 GLY44 LEU45 GLU46 TRP47 ASN52 ASN57 HIS59 THR61 TYR95 HIS99 TYR102 ASP103 LYS104 TYR105 PRO107 CYS108 PHE111 ALA112 GLY113 TYR115 THR116 TRP118 GLY119 GLN120 C: ARG346 SER349 TYR351 ALA352 ARG403 ASP405 GLU406 ARG408 GLN409 GLY416 LYS417 ILE418 LYS444 VAL445 GLY446 GLY447 TYR449 ASN450 LEU452 TYR453 LEU455 PHE456 ARG466 ILE468 THR470 ILE472 GLY482 VAL483 GLU484 GLY485 PHE486 CYS488 TYR489 PHE490 LEU492 GLN493 SER494 TYR495 GLY496 GLN498 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)
