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Entry information

Complex
AACDB_ID: 7205
PDBID: 7MDW
Chains: A_R
Organism: Lama glama, Severe acute respiratory syndrome coronavirus 2
Method: EM
Resolution (Å): 3.58
Reference: 10.1038/s41467-021-24963-3
Antibody
Antibody: 21 Nanobody
Antibody mutation: No
INN (Clinical Trial):
Antigen
Antigen: SARS-CoV-2 spike glycoprotein RBD
Antigen mutation: No
Durg Target: P0DTC2; P0DTC2;

Sequence information

Antibody

Chain: A
Mutation: NULL

>7MDW_A|Chain A|nonobody Nb21|Lama glama (9844)
QVQLVESGGGLVQAGGSLRLSCAVSGLGAHRVGWFRRAPGKEREFVAAIGANGGNTNYLDSVKGRFTISRDNAKNTIYLQMNSLKPQDTAVYYCAARDIETAEYTYWGQGTQVTVSS

Antigen

Chain: R
Mutation: NULL

>7MDW_R|Chain B[auth R]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049)
TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCG

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)

A: GLY28 ALA29 ARG31 PHE35 PHE45 ALA48 ALA51 ASN52 ASN55 ASN57 LEU59 ASN72 ARG97 ILE99 GLU100 THR101 ALA102

R: GLY446 TYR449 ASN450 LEU452 PHE456 ILE472 VAL483 GLU484 GLY485 PHE486 ASN487 TYR489 PHE490 LEU492 GLN493 SER494 GLY496

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)

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