SMTL ID : 8owv.1

H6 and F2 nanobodies bound to SARS-CoV-2 spike RBD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: F.8, G.9, F.12, N.13, V.37 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.8, A:F.12, A:V.37 Water bridges: A:G.9, A:G.9, A:N.13, A:N.13

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: F.12, N.13, S.43, F.44, W.106 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.12 GOL.3: 2 residues within 4Å: Chain A: A.42, S.43 No protein-ligand interaction detected (PLIP) GOL.4: 4 residues within 4Å: Chain A: G.51 Chain B: H.30, S.31, W.53 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.30, B:H.30, A:G.51 Water bridges: B:W.53, B:R.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cornish, K. et al., Structural and functional characterization of nanobodies that neutralize Omicron variants of SARS-CoV-2. Open Biology (2024)

Release Date

2024-05-08

Peptides

Spike protein S1: A
F2: B
H6: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
EEE

B
BBB

C
FFF

Spike protein S1

F2

H6

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