SMTL ID : 7z1e.1

Nanobody H11-H4 Q98R H100E bound to RBD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: G.10, N.14, V.38, L.39 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.39 Water bridges: A:G.10, A:N.14

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: W.24, N.25, R.26, R.137 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.24, A:R.26 Water bridges: A:R.137 GOL.3: 5 residues within 4Å: Chain A: R.26, Y.67, F.135, S.185, E.187 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.26, A:R.26, A:S.185, A:S.185 GOL.4: 5 residues within 4Å: Chain A: F.13, N.14, S.44, F.45, W.107 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.14, A:S.44

2 x NO3: NITRATE ION(Non-functional Binders)

NO3.5: 3 residues within 4Å: Chain A: H.190, A.191 Ligands: NO3.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.190 NO3.6: 2 residues within 4Å: Chain A: R.28 Ligands: NO3.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.28 Water bridges: A:N.65, A:N.65

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-H4 Q98R H100E: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
EEE

B
FFF

Spike protein S1

H11-H4 Q98R H100E

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