SMTL ID : 5f0e.1

Murine endoplasmic reticulum alpha-glucosidase II

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.74 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.241, G.282, P.283, S.284, D.287, Q.291 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.287

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

PG4.2: 3 residues within 4Å: Chain A: V.817, E.825, R.827 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.825 Water bridges: A:R.857, A:R.857 PG4.3: 5 residues within 4Å: Chain A: N.333, D.608, R.611, D.612, F.615 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.615 Hydrogen bonds: A:D.608, A:R.611 Water bridges: A:N.333, A:D.608, A:R.611 PG4.4: 7 residues within 4Å: Chain A: Q.831, I.840 Chain B: Y.26, C.27, D.28, C.29, K.30 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:Y.26, A:Q.831

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

P6G.5: 7 residues within 4Å: Chain A: S.651, S.654, I.655, E.656, D.657, Y.681, T.703 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.656, A:D.657 P6G.6: 16 residues within 4Å: Chain A: R.17, Q.18, S.20, I.21, L.25, S.26, P.27, Y.28, H.48, V.50, G.142, L.143, M.144, A.145, F.146, E.147 No protein-ligand interaction detected (PLIP) P6G.7: 8 residues within 4Å: Chain A: P.79, R.80, Y.81, R.82, P.84, Y.476, G.477, W.479 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.82, A:W.479

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

EDO.8: 3 residues within 4Å: Chain A: D.318, T.357, R.358 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.318, A:D.318 Water bridges: A:E.319 EDO.9: 5 residues within 4Å: Chain A: E.395, W.433, N.436, M.437, N.442 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.433 EDO.10: 7 residues within 4Å: Chain A: D.612, Q.616, Q.693, S.711, S.712, I.713, P.714 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.612, A:Q.616, A:I.713 Water bridges: A:I.713

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

FMT.11: 5 residues within 4Å: Chain A: R.397, K.404, G.408, S.409, D.410 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.404, A:G.408, A:D.410 FMT.12: 7 residues within 4Å: Chain A: R.718, G.719, G.720, S.748, Q.750, T.752, Q.754 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.718, A:R.718, A:S.748, A:T.752 Water bridges: A:G.720 FMT.13: 5 residues within 4Å: Chain A: Y.646, E.648, D.649, G.684, Q.685 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.685 Water bridges: A:Y.646, A:D.649 FMT.14: 6 residues within 4Å: Chain A: F.615, M.727, R.728, V.729 Chain B: P.42, S.61 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.729, A:V.729 FMT.15: 7 residues within 4Å: Chain A: A.534, E.535, W.536, N.567, P.568, E.569, L.572 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.534, A:E.569 Water bridges: A:W.536 FMT.16: 4 residues within 4Å: Chain A: I.692, R.725, M.727, F.744 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Y.695, A:Y.695, A:R.725 FMT.17: 3 residues within 4Å: Chain A: T.298, H.632, K.633 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.298, A:T.298, A:K.633 FMT.18: 3 residues within 4Å: Chain A: F.286, R.290, F.636 No protein-ligand interaction detected (PLIP) FMT.19: 9 residues within 4Å: Chain A: Y.690, Y.695, Q.696, K.697, M.808, G.809, T.836, S.837, V.838 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.697, A:G.809 FMT.20: 6 residues within 4Å: Chain A: R.141, L.143, E.204, D.256, S.258, R.267 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.141, A:R.141 Water bridges: A:S.258, A:S.258, A:R.267 FMT.21: 3 residues within 4Å: Chain A: N.5, F.462, V.467 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.5

2 x CA: CALCIUM ION(Non-covalent)

CA.22: 8 residues within 4Å: Chain A: R.842 Chain B: Q.21, D.24, Y.26, C.27, 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.23: 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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