Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6500 |
| PDBID: | 7R4I |
| Chains: | D_A |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Camelus dromedarius |
| Method: | EM |
| Resolution (Å): | 3.20 |
| Reference: | 10.3389/fimmu.2022.863831 |
| Antibody | |
| Antibody: | 2.15 Nanobody |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 spike glycoprotein |
| Antigen mutation: | No |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Chain: D
Mutation: NULL
| >7R4I_D|Chain D, E|Camel-derived nanobody 2.15|Camelus dromedarius (9838) QVQLVESGGGSVQAGGSLKLSCAASGYASWARKCIGWFRQAPGQEREGVAAIFDFDGSTYYSDSVKGRFTISGDNAKNTVSLQMNSLLPKDTAVYYCTVAFGTCDNWYRGRGDYWGQGTQVTVSSALVPR |
Antigen
Chain: A
Mutation: NULL
| >7R4I_A|Chain A, B, C|Spike glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049) MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQGSGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGTENLYFQGDYKDDDDKGSHHHHHH |
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: GLN1 ALA28 SER29 TRP30 ALA31 ARG32 LYS33 PHE55 ASP56 GLY57 SER72 GLY73 ASP74 ASN75 ALA76 LYS77 PHE101 GLY102 THR103 TYR114 A: ARG403 GLY446 TYR449 LEU452 LEU455 PHE456 ILE472 TYR473 ALA475 GLU484 GLY485 PHE486 TYR489 PHE490 PRO491 LEU492 GLN493 SER494 TYR495 GLN498 THR500 ASN501 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)
