Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5522 |
| PDBID: | 7X2K |
| Chains: | HL_E |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens, Vicugna pacos |
| Method: | XRD |
| Resolution (Å): | 2.40 |
| Reference: | 10.1038/s41467-022-35642-2 |
| Antibody | |
| Antibody: | 1F11 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | Amubarvimab(Phase-II/III) |
| Antigen | |
| Antigen: | SARS-CoV-2 spike glycoprotein RBD |
| Antigen mutation: | No |
| Durg Target: | P0DTC2; P0DTC2; |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >7X2K_H|Chain B[auth H]|1F11-H|Homo sapiens (9606) EVQLVESGGGLVQPGGSLRLSCAASGITVSSNYMNWVRQAPGKGLEWVSLIYSGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYHCARDLVVYGMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP |
Light Chain: L
Mutation: NULL
| >7X2K_L|Chain C[auth L]|1F11-L|Homo sapiens (9606) EIVLTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: E
Mutation: NULL
| >7X2K_E|Chain A[auth E]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCG |
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: VAL2 GLY26 ILE27 THR28 SER30 SER31 ASN32 TYR33 LEU50 TYR52 SER53 GLY54 SER56 TYR58 ARG97 LEU99 VAL100 VAL101 TYR102 ASP105 VAL106 L: GLU1 ILE2 GLN27 SER28 VAL29 SER30 SER31 SER32 TYR33 SER68 GLY69 GLN91 TYR92 GLY93 SER94 E: ARG403 ASP405 THR415 GLY416 LYS417 ASP420 TYR421 TYR449 TYR453 LEU455 PHE456 ARG457 LYS458 SER459 ASN460 TYR473 GLN474 ALA475 GLY476 SER477 GLU484 PHE486 ASN487 TYR489 PHE490 GLN493 SER494 TYR495 GLY496 GLN498 THR500 ASN501 GLY502 VAL503 GLY504 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)
