Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6056 |
| PDBID: | 8DW9 |
| Chains: | CD_B |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 4.00 |
| Reference: | 10.1080/22221751.2022.2146538 |
| Antibody | |
| Antibody: | D29 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 spike glycoprotein RBD |
| Antigen mutation: | No |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: C
Mutation: NULL
| >8DW9_C|Chain C, E[auth H]|D29 Heavy chain|Homo sapiens (9606) QLVESGAEVKKPGSSVKVSCKASGDTFYTFDISWVRQAPGQGLEWMGGISPVFDAPNYAQKFQDRVTITADKSTSTAYMELSSLRSEDTAIYYCVKPTYSNYVWGIGAFDVWGQGTTVTVSSASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKAA |
Light Chain: D
Mutation: NULL
| >8DW9_D|Chain D, F[auth L]|D29 Fab light chain|Homo sapiens (9606) EIVLTQSPGTLSLSPGERATLSCRASQSVGNIYLAWYQQKPGQAPRLLIYGASTRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGDSLWTFGQGTKVEIKGQPKANPTVTLFPPSSEELQANKATLVCLIDNFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT |
Antigen
Chain: B
Mutation: NULL
| >8DW9_B|Chain A, B|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGP |
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)
| C: THR31 PHE54 ALA56 ASN58 GLN61 GLN64 TYR97 SER98 ASN99 D: GLY29 ILE31 TYR32 GLY92 ASP93 SER94 B: LEU335 PHE338 GLY339 GLU340 PHE342 ASN343 ALA344 THR345 ARG346 VAL367 LEU368 SER373 PHE374 ASN440 LEU441 LYS444 VAL445 ASN450 ARG509 |
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)
