Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 4092 |
| PDBID: | 7LDJ |
| Chains: | E_B |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Vicugna pacos |
| Method: | XRD |
| Resolution (Å): | 2.36 |
| Reference: | 10.1073/pnas.210191811 |
| Antibody | |
| Antibody: | 7LDJ_2 Nanobody |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Spike glycoprotein RBD |
| Antigen mutation: | No |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Chain: E
Mutation: NULL
| >7LDJ_E|Chain E, F, G, H|Nanobody 2|Vicugna pacos (30538) QVQLQESGGGLVQPGGSLRLSCAVSGFTLDYYAIGWFRQAPGKEREGVSCISSSGGNTKYADSVKGRFTASRDNAKNTFYLQMNSLKPEDTAVYYCAAIAATYYSGSYYFQCPHDGMDYWGKGTQVTVSSH |
Antigen
Chain: B
Mutation: NULL
| >7LDJ_B|Chain A, B, C, D|Spike glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049) NITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPGS |
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 E: GLN1 PHE27 THR28 LEU29 ASP30 TYR31 GLY47 VAL48 SER49 CYS50 LYS58 TYR59 ALA60 ASP61 ILE95 ALA96 ALA97 THR98 TYR99 TYR100 TYR104 TYR105 PHE106 GLN107 CYS108 PRO109 HIS110 ASP111 GLY112 MET113 ASP114 TYR115 B: TYR351 ARG403 LYS417 VAL445 GLY446 GLY447 TYR449 ASN450 LEU452 TYR453 LEU455 PHE456 ILE468 THR470 ILE472 THR478 GLU484 GLY485 PHE486 TYR489 PHE490 LEU492 GLN493 SER494 TYR495 GLY496 GLN498 THR500 ASN501 GLY502 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)
