Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 4470 |
| PDBID: | 7NP1 |
| Chains: | JN_C |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 2.80 |
| Reference: | 10.3389/fimmu.2021.678570 |
| Antibody | |
| Antibody: | ION-360 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: J
Mutation: NULL
| >7NP1_J|Chain E[auth H], F[auth I], G[auth J], H[auth K]|Immunoglobulin gamma-1 heavy chain|Homo sapiens (9606) EVQLVQSGGGLVKPGGSLRLSCAASGITVSSNYMSWVRQAPGKGLEWVSVIYSGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARGEGGSIVGVTSDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC |
Light Chain: N
Mutation: NULL
| >7NP1_N|Chain I[auth L], J[auth M], K[auth N], L[auth O]|Immunoblobulin light chain|Homo sapiens (9606) ASDIQMTQSPSSLSASVGDRVTITCRASQSISRYLNWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSETEFTLTISSLHPDDFATYYCQQSYSTLPYTFGQGTKVEIKRTAAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKLYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: C
Mutation: NULL
| >7NP1_C|Chain A, B, C, D|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLPATVCGPKKSTNLVKNKCVNFAAAGSHHHHHH |
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)
| Chain residues position delta_SASA
: residuesposition J: GLU1 VAL2 GLY26 ILE27 THR28 SER30 SER31 ASN32 TYR33 TYR52 SER53 GLY54 SER56 THR57 TYR58 ARG97 GLU99 ILE103 VAL104 GLY105 VAL106 TYR110 N: SER28 SER30 TYR32 SER56 GLU68 SER91 TYR92 THR94 C: ARG403 ASP405 ARG408 THR415 GLY416 LYS417 ASP420 TYR421 TYR453 LEU455 PHE456 ARG457 LYS458 SER459 ASN460 TYR473 GLN474 ALA475 GLY476 SER477 PHE486 ASN487 TYR489 GLN493 GLN498 THR500 ASN501 GLY502 GLY504 TYR505 |
2、We defined interacting paratope-epitope residues by a distance cutoff of < 6 Å . Two amino acids are considered as interacting residues if they have at least one atom within a distance of 6 Å from any atom.
Interacting residues (Atom distance based)
