Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6511 |
| PDBID: | 7RBY |
| Chains: | B_A |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Lama glama |
| Method: | XRD |
| Resolution (Å): | 2.82 |
| Reference: | 10.1080/19420862.2022.2047144 |
| Antibody | |
| Antibody: | nb112 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: B
Mutation: NULL
| >7RBY_B|Chain B, D|Ilama-isolated nanobody NIH-CoV nb-112 specific to SARS-CoV-2 RBD|Lama glama (9844) DVQLQESGGGLVQPGGSLRLSCAASGLTLDYYAIGWFRQAPGKEREGVSCISSSDGSTYYADSVKGRFTTSRDNAKNTVYLQMNSLKPEDTAVYYCAAVPSTYYSGTYYYTCHPGGMDYWGKGTQVTVSS |
Antigen
Chain: A
Mutation: NULL
| >7RBY_A|Chain A, C|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) FPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKC |
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 B: ASP1 VAL2 THR28 LEU29 ASP30 TYR31 PHE37 GLY47 VAL48 SER49 TYR58 TYR59 ALA60 ASP61 LYS64 VAL95 PRO96 SER97 THR98 TYR99 MET100 ASP101 TYR102 A: TYR351 ARG403 LYS417 VAL445 GLY446 GLY447 TYR449 LEU452 TYR453 LEU455 PHE456 ILE468 THR470 ILE472 TYR473 VAL483 GLU484 GLY485 PHE486 ASN487 TYR489 PHE490 LEU492 GLN493 SER494 TYR495 GLY496 GLN498 THR500 ASN501 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)
