Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5508 |
| PDBID: | 7X1M |
| Chains: | CD_M |
| Organism: | Homo sapiens, Severe acute respiratory syndrome coronavirus 2 |
| Method: | EM |
| Resolution (Å): | 2.74 |
| Reference: | 10.1016/j.immuni.2022.06.005 |
| Antibody | |
| Antibody: | BD604 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Omicron BA.1 spike glycoprotein RBD |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2; P0DTC2; P0DTC2; |
Sequence information
Antibody
Heavy Chain: C
Mutation: NULL
| >7X1M_C|Chain C|BD-604 Fab heavy chain|Homo sapiens (9606) EVQLVESGGGLIQPGGSLRLSCAASGIIVSSNYMTWVRQAPGKGLEWVSVIYSGGSTFYADSVKGRFTISRDNSKNTLYLQMSSLRAEDTAVYYCARDLGPYGMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK |
Light Chain: D
Mutation: NULL
| >7X1M_D|Chain D|BD-604 Fab light chain|Homo sapiens (9606) DIQLTQSPSFLSASVGDRVTITCRASQGISSDLAWYQQKPGKAPNLLIYAASTLQSGVPSRFSGSGSGTEFTLTISSLQPEDFATYYCQQLNSDLYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: M
Mutation: G7D/S39L/S41P/S43F/K85N/N108K/G114S/S145N/T146K/E152A/Q161R/G164S/Q166R/N169Y/Y173H
| >7X1M_M|Chain G[auth M]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) TNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNF |
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: VAL2 GLY26 ILE27 ILE28 SER30 SER31 ASN32 TYR33 TYR52 SER53 GLY54 SER56 PHE58 ARG97 LEU99 GLY100 PRO101 TYR102 ASP105 VAL106 D: GLN27 GLY28 ILE29 SER30 SER31 ASP32 ALA50 SER67 GLY68 LEU91 ASN92 SER93 ASP94 M: ARG403 ASP405 GLU406 ARG408 GLN409 THR415 GLY416 ASN417 ASP420 TYR421 TYR453 LEU455 PHE456 ARG457 LYS458 SER459 ASN460 TYR473 GLN474 ALA475 GLY476 ASN477 LYS478 PHE486 ASN487 TYR489 PHE490 LEU492 ARG493 TYR495 ARG498 THR500 TYR501 GLY502 VAL503 GLY504 HIS505 |
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)
