Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5959 |
| PDBID: | 8DCC |
| Chains: | HL_E |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 2.60 |
| Reference: | 10.1126/sciadv.abq8276 |
| Antibody | |
| Antibody: | P2B-2F6 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 spike glycoprotein RBD SPEEDesign immunogen 3 |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >8DCC_H|Chain C[auth H]|P2B-2F6 Fab heavy chain|Homo sapiens (9606) QVQLQESGPGLVKPSETLSLTCTVSGYSISSGYYWGWIRQPPGKGLEWIGSIYHSGSTYYNPSLKTRVTISVDTSKNQFSLKLSSVTAADTAVYYCARAVVGIVVVPAAGRRAFDIWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTGGSHHHHHH |
Light Chain: L
Mutation: NULL
| >8DCC_L|Chain B[auth L]|P2B-2F6 Fab light chain|Homo sapiens (9606) QSALTQPPSASGSPGQSVTISCTGTSSDVGGYNYVSWYQQHPGKAPKLMIYEVSKRPSGVPDRFSGSKSGNTASLTVSGLQAEDEADYYCSSYAGSNNLVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS |
Antigen
Chain: E
Mutation: T4K/A34Y/N59K/N65Y/I139T/S185T/H190D/A193P
| >8DCC_E|Chain A[auth E]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) ETGKNLCPFGEVFNATRFASVYAWNRKRISNCVYDYSVLYNSASFSTFKCYGVSPTKLKDLCFTYVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDTSTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLTFELLDAPPTVCGGTGGGGSKHHHHHH |
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)
| L: GLY31 TYR32 ASN33 TYR34 GLU52 H: GLY26 TYR27 SER28 SER30 SER31 GLY32 TYR33 HIS54 GLY102 ILE103 VAL104 VAL105 VAL106 PRO107 ARG112 E: ARG346 TYR351 LYS444 VAL445 GLY446 GLY447 ASN448 TYR449 ASN450 LEU452 THR470 ILE472 VAL483 GLU484 GLY485 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)
