SMTL ID : 8bev.1

Cryo-EM structure of SARS-CoV-2 spike (HexaPro variant) in complex with nanobody W25 (map 3, focus refinement on RBD, W25 and adjacent NTD)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-mer

Ligands

3 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 3 residues within 4Å: Chain C: E.132, N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 7 residues within 4Å: Chain C: V.120, N.122, T.124, N.125, L.141, E.154, S.155 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 2 residues within 4Å: Chain C: E.281, N.282 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.4: 5 residues within 4Å: Chain A: F.342, N.343, V.367, N.370, S.371 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.370, A:S.371

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.5: 2 residues within 4Å: Chain C: N.234, T.236 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Modhiran, N. et al., A nanobody recognizes a unique conserved epitope and potently neutralizes SARS-CoV-2 omicron variants. Iscience (2023)

Release Date

2023-03-08

Peptides

Spike glycoprotein: AC
immunoglobulin mu heavy chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

Spike glycoprotein

immunoglobulin mu heavy chain

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