SMTL ID : 5iee.1

Murine endoplasmic reticulum alpha-glucosidase II with 1-deoxynojirimycin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

hetero-1-1-mer

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: 11 residues within 4Å: Chain A: K.64, N.65, P.114, Y.115, E.130, R.299, G.359, P.360, S.361, D.364, Q.368 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.364

3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.2: 3 residues within 4Å: Chain A: V.894, E.902, R.904 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.902 Water bridges: A:R.904 PG4.3: 5 residues within 4Å: Chain A: N.410, D.685, R.688, D.689, F.692 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.685 Water bridges: A:N.410, A:D.685 PG4.4: 10 residues within 4Å: Chain A: T.375, Y.706, H.709, K.710, Y.844, Q.845, H.848, F.850, D.868, K.870 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.706, A:K.710, A:K.710

4 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.5: 7 residues within 4Å: Chain A: S.728, S.731, I.732, E.733, D.734, Y.758, T.780 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.728 Water bridges: A:E.733, A:D.734, A:D.734 P6G.6: 14 residues within 4Å: Chain A: R.17, Q.18, S.20, I.21, P.27, Y.28, H.48, V.50, G.142, L.143, M.144, A.145, F.146, E.147 3 PLIP interactions: 3 interactions with chain A Water bridges: A:H.48, A:H.48, A:H.48 P6G.7: 8 residues within 4Å: Chain A: P.79, R.80, Y.81, R.82, P.84, Y.553, G.554, W.556 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.82, A:W.556 Water bridges: A:R.80, A:R.80 P6G.23: 14 residues within 4Å: Chain A: Y.772, M.804, F.821, R.881, V.883, Q.908, I.917 Chain B: Y.26, C.27, D.28, C.29, K.30, C.41, P.42 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Y.26

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 3 residues within 4Å: Chain A: D.395, T.434, P.437 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.395, A:D.395 EDO.9: 5 residues within 4Å: Chain A: E.472, W.510, N.513, M.514, N.519 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.472, A:W.510 Water bridges: A:R.468 EDO.10: 6 residues within 4Å: Chain A: D.689, Q.693, Q.770, S.788, S.789, I.790 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.693, A:I.790 Water bridges: A:Q.770, A:I.790 EDO.11: 5 residues within 4Å: Chain A: W.878, K.920, G.922 Chain B: D.24, D.25 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.24, A:K.920 Water bridges: A:G.922 EDO.12: 5 residues within 4Å: Chain A: L.440, F.517, S.523, A.524, P.525 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.523 EDO.26: 7 residues within 4Å: Chain A: A.447, S.448, R.450 Chain B: G.66, V.67, C.68, T.81 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.66

10 x FMT: FORMIC ACID(Non-functional Binders)

FMT.13: 6 residues within 4Å: Chain A: R.795, G.797, S.825, Q.827, T.829, Q.831 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.795, A:R.795 FMT.14: 5 residues within 4Å: Chain A: Y.723, E.725, D.726, G.761, Q.762 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.762 Water bridges: A:E.725, A:D.726 FMT.15: 6 residues within 4Å: Chain A: F.692, M.804, R.805, V.806 Chain B: P.42, S.61 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:M.804, A:V.806 Water bridges: B:S.61 FMT.16: 7 residues within 4Å: Chain A: A.611, E.612, W.613, N.644, P.645, E.646, L.649 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.611, A:E.646, A:E.646 Water bridges: A:W.613 FMT.17: 3 residues within 4Å: Chain A: F.363, R.367, F.713 No protein-ligand interaction detected (PLIP) FMT.18: 9 residues within 4Å: Chain A: Y.767, Y.772, Q.773, K.774, M.885, G.886, T.913, S.914, V.915 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.774, A:G.886 FMT.19: 7 residues within 4Å: Chain A: R.141, L.143, E.262, D.314, I.315, S.316, R.344 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.141, A:R.141, A:S.316 Water bridges: A:D.314, A:D.314 FMT.20: 3 residues within 4Å: Chain A: N.5, F.539, V.544 No protein-ligand interaction detected (PLIP) FMT.21: 4 residues within 4Å: Chain A: R.390, N.392, R.394, R.673 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.390, A:R.390, A:N.392, A:R.394, A:R.673 Water bridges: A:N.392, A:N.392 FMT.27: 6 residues within 4Å: Chain B: P.36, G.37, S.45, F.46, H.47, Y.57 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.47

1 x NOJ: 1-DEOXYNOJIRIMYCIN(Non-covalent)

NOJ.22: 15 residues within 4Å: Chain A: W.391, D.419, I.420, I.456, W.493, W.530, D.532, M.533, R.592, W.605, G.607, D.608, F.641, R.664, H.666 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.419, A:D.419, A:W.493, A:D.532, A:D.532, A:R.592, A:D.608, A:H.666 Water bridges: A:W.605

2 x CA: CALCIUM ION(Non-covalent)

CA.24: 7 residues within 4Å: Chain A: R.919 Chain B: Q.21, D.24, Y.26, D.28, D.34, E.35 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:Q.21, B:D.24, B:Y.26, B:D.28, B:D.34, B:E.35 CA.25: 6 residues within 4Å: Chain B: R.62, D.65, V.67, D.69, D.75, E.76 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:R.62, B:D.65, B:V.67, B:D.69, B:D.75, B:E.76

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Caputo, A.T. et al., Structures of mammalian ER alpha-glucosidase II capture the binding modes of broad-spectrum iminosugar antivirals. Proc.Natl.Acad.Sci.USA (2016)

Release Date

2016-07-27

Peptides

Neutral alpha-glucosidase AB: A
Glucosidase 2 subunit beta: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Neutral alpha-glucosidase AB

Glucosidase 2 subunit beta

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