SMTL ID : 5mhf.1 (3 other biounits)

Murine endoplasmic reticulum alpha-glucosidase I with N-9'-methoxynonyl-1-deoxynojirimycin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 4 residues within 4Å: Chain A: H.532, N.599, P.623, L.625 No protein-ligand interaction detected (PLIP)

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: H.201, S.203, Q.230, H.231, R.232 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.230, A:R.232 Water bridges: A:Y.241 Salt bridges: A:H.201 SO4.3: 3 residues within 4Å: Chain A: R.503, R.505, G.506 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.506 Water bridges: A:R.503, A:R.503, A:R.503, A:S.534 Salt bridges: A:R.503 SO4.5: 1 residues within 4Å: Chain A: R.683 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.683

1 x 6A9: N-9'-methoxynonyl-1-deoxynojirimycin(Non-covalent)

6A9.4: 15 residues within 4Å: Chain A: P.381, S.384, F.385, F.386, R.388, F.390, W.392, D.393, E.429, G.523, D.525, Y.691, W.692, F.764, W.767 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.385, A:F.390 Hydrogen bonds: A:F.386, A:W.392, A:D.393 Water bridges: A:E.749 Salt bridges: A:D.393, A:D.525, A:E.749

1 x 7PG: 2,5,8,11,14,17,20,23-OCTAOXAPENTACOSAN-25-OL(Non-covalent)

7PG.6: 6 residues within 4Å: Chain A: W.8, R.12, L.15, L.17, P.372, P.373 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Warfield, K.L. et al., Targeting Endoplasmic Reticulum alpha-Glucosidase I with a Single-Dose Iminosugar Treatment Protects against Lethal Influenza and Dengue Virus Infections. J.Med.Chem. (2020)

Release Date

2017-12-20

Peptides

Mannosyl-oligosaccharide glucosidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Mannosyl-oligosaccharide glucosidase

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