SMTL ID : 5kwb.1

Crystal Structure of the Receptor Binding Domain of the Spike Glycoprotein of Human Betacoronavirus HKU1 (HKU1 1A-CTD, 1.9 angstrom, molecular replacement)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

monomer

Ligands

1 x GLC- FRU: beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose(Non-covalent)

GLC-FRU.1: 4 residues within 4Å: Chain A: V.332, Y.336, N.364 Ligands: MG.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.364

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

NAG.2: 3 residues within 4Å: Chain A: F.30, I.126, N.127 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.30 Hydrogen bonds: A:N.127 NAG.3: 4 residues within 4Å: Chain A: N.164, N.165, T.166, N.194 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.166 Hydrogen bonds: A:N.164, A:T.166, A:T.166 NAG.4: 1 residues within 4Å: Chain A: N.148 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.148 NAG.5: 5 residues within 4Å: Chain A: D.20, N.49, T.52, N.301, D.302 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.49, A:T.52

6 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 1 residues within 4Å: Chain A: R.225 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain A: R.91, F.102, Y.156, R.158 No protein-ligand interaction detected (PLIP) MG.8: 5 residues within 4Å: Chain A: V.332, N.364, F.366 Ligands: GLC-FRU.1, GLC-FRU.1 No protein-ligand interaction detected (PLIP) MG.9: 5 residues within 4Å: Chain A: F.167, C.168, R.196, S.197, S.228 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain A: C.21, K.41, F.43 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.21, H2O.8 MG.11: 7 residues within 4Å: Chain A: R.40, V.81, L.82, D.83, Y.108, N.287, I.289 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.83

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ou, X. et al., Crystal structure of the receptor binding domain of the spike glycoprotein of human betacoronavirus HKU1. Nat Commun (2017)

Release Date

2017-06-07

Peptides

Spike glycoprotein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Spike glycoprotein

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