Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6057 |
| PDBID: | 8DWA |
| Chains: | HL_A |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 3.20 |
| Reference: | 10.1080/22221751.2022.2146538 |
| Antibody | |
| Antibody: | P1D9 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: H
Mutation: NULL
| >8DWA_H|Chain B[auth H]|P1D9 Heavy chain|Homo sapiens (9606) VQLVQSGAEVKKPGSSVRVSCKASGGTFGDDSITWVRQAPGQGLEWMGGIFPLIGKTHYAQRFQGRLTVTADKSTSTAYMELSGLRSEDTAIYYCARDTGWTLTAFDIWGQGTMVTVSSASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK |
Light Chain: L
Mutation: NULL
| >8DWA_L|Chain C[auth L]|P1D9 Light chain|Homo sapiens (9606) DIQMTQSPSSLSASVGDTVTITCRAGQTINTFLNWYQQKPGKAPKLLIYAASTLQSGVPSRFSGSGSGTDFTLTINSLQPEDFATYYCQQSYSNLYTFSQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR |
Antigen
Chain: A
Mutation: NULL
| >8DWA_A|Chain A|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) LCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSF |
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: SER33 TRP47 GLY50 LEU53 ILE54 LYS56 THR57 HIS58 TYR59 GLN64 TRP98 THR99 L: THR28 ILE29 ASN30 PHE32 GLN90 SER91 TYR92 SER93 ASN94 LEU95 A: GLU340 ASN343 ALA344 THR345 ARG346 SER349 TYR351 ASN440 LEU441 ASP442 SER443 LYS444 VAL445 GLY446 GLY447 ASN448 TYR449 ASN450 LEU452 ILE468 THR470 GLU484 PHE490 LEU492 GLN493 SER494 GLY496 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)
