SMTL ID : 7z1d.1

Nanobody H11-H6 bound to RBD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

hetero-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.9, G.10, N.14, V.38, L.39 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.38, A:L.39 Water bridges: A:G.10, A:G.10, A:N.14

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: W.24, R.26, F.135 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mikolajek, H. et al., Correlation between the binding affinity and the conformational entropy of nanobody SARS-CoV-2 spike protein complexes. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-03-23

Peptides

Spike protein S1: A
H11-H6 nanobody: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
EEE

B
FFF

Spike protein S1

H11-H6 nanobody

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