SMTL ID : 8owt.2 (1 other biounit)

SARS-CoV-2 spike RBD with A8 and H3 nanobodies bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.37 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 B: F.9, G.10, F.13, N.14, L.39 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.9, B:F.13, B:L.39

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.2: 3 residues within 4Å: Chain B: W.24, R.26, F.135 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.26

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

Nanobody A8: A
Spike protein S1: B
Nanobody H3: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
DDD

B
EEE

C
FFF

Nanobody A8

Spike protein S1

Nanobody H3

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