Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5432 |
| PDBID: | 7WQV |
| Chains: | F_E |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 2.80 |
| Reference: | 10.1371/journal.ppat.1011085 |
| Antibody | |
| Antibody: | Ab08 scFv |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Wuhan-hu-1 spike glycoprotein RBD |
| Antigen mutation: | No |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Chain: F
Mutation: NULL
| >7WQV_F|Chain B, D, F, H, J, L, N, P|Ab08|Homo sapiens (9606) MSKYLLPTAAAGLLLLAAQPAMAGSSSQVQLVQSGAEVKKPGSSVKVSCKASGGTFSSYTISWVRQAPGQGLEWMGGIIPILGTTNYAQKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCARKFGYSGYGATWYFDLWGRGTLVTVSSGGGGSGGGGSGGGGSQSVLTQPPSVSGAPGQRVTISCTGNSSNIGAGYDVHWYQQFPGTAPKLLIYGNSNRPSGVPDRFSGSKSGTSASLAITGLQAEDEADYYCQSYDSSLSGSVFGGGTKLTVLAGRAGEQKLISEEDLNSAVDHHHHHH |
Antigen
Chain: E
Mutation: NULL
| >7WQV_E|Chain A, C, E, G, I, K, M, O|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) MKFLVNVALVFMVVYISYIYAAGSPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTGTLEVLFQ |
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)
| F: THR28 SER30 SER31 THR33 ILE52 ILE54 LEU55 THR57 THR58 ASN59 TYR60 GLN62 GLN65 ARG98 LYS99 PHE100 GLY101 TYR102 SER103 GLY104 TYR105 GLY106 ALA107 THR108 TRP109 SER1026 SER1027 GLY1030 ALA1031 TYR1033 THR1071 TYR1093 SER1095 SER1096 LEU1097 SER1098 E: GLU340 THR345 ARG346 PHE347 ALA348 TYR351 ALA352 TRP353 ASN354 ARG355 LYS356 ARG357 SER359 TYR396 TYR449 ASN450 LEU452 ARG457 LYS462 PRO463 PHE464 GLU465 ARG466 ASP467 ILE468 SER469 THR470 GLU471 ILE472 GLY482 VAL483 GLU484 PHE490 LEU492 GLN493 SER494 |
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)
