Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5978 |
| PDBID: | 8DF5 |
| Chains: | HL_R |
| Organism: | Homo sapiens, Severe acute respiratory syndrome coronavirus 2 |
| Method: | XRD |
| Resolution (Å): | 2.70 |
| Reference: | 10.1126/science.abo7896 |
| Antibody | |
| Antibody: | S304 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Beta spike glycoprotein RBD |
| Antigen mutation: | No |
| Durg Target: | P0DTC2; P0DTC2; |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >8DF5_H|Chain G[auth H], I[auth M]|S304 Fab Heavy Chain|Homo sapiens (9606) QVQLVESGGGLVQPGGSLRLSCAASGFTFSSYDMHWVRQTTGKGLEWVSTIGTAGDTYYPDSVKGRFTISREDAKNSLYLQMNSLRAGDTAVYYCARGDSSGYYYYFDYWGQGTLLTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKAC |
Light Chain: L
Mutation: NULL
| >8DF5_L|Chain H[auth L], J[auth N]|S304 Fab Light Chain|Homo sapiens (9606) DIQMTQSPSSLSAAVGDRVTITCRASQSIGSYLNWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFAIYYCQQSYVSPTYTFGPGTKVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: R
Mutation: NULL
| >8DF5_R|Chain K[auth R], L[auth S]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) MGILPSPGMPALLSLVSLLSVLLMGCVAETGTRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVKGFNCYFPLQSYGFQPTYGVGYQPYRVVVLSFELLHAPATVCGPKKSTHHHHHHHHGGSSGLNDIFEAQKIEWHE |
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: SER31 TYR32 ASP33 THR50 GLY52 THR53 ALA54 GLY55 ASP56 THR57 TYR58 ASP61 LYS64 ASP99 SER100 TYR103 TYR105 L: ASP1 GLN27 SER28 TYR32 TYR92 VAL93 SER94 PRO95 THR96 TYR97 R: SER366 TYR369 ASN370 SER371 ALA372 PHE374 SER375 PHE377 LYS378 CYS379 TYR380 GLY381 VAL382 SER383 PRO384 THR385 LYS386 ASN388 ASP389 LEU390 CYS391 PHE392 PRO412 GLY413 GLN414 ASP427 ASP428 PHE429 THR430 LEU517 LYS528 |
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)
