SMTL ID : 5h9o.2 (1 other biounit)

Complex of Murine endoplasmic reticulum alpha-glucosidase II with D-Glucose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.37 Å

Oligo State

hetero-1-1-mer

Ligands

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Non-functional Binders)

NAG.1: 10 residues within 4Å: Chain A: K.64, N.65, Y.115, E.130, R.241, G.282, P.283, D.287, Q.291 Ligands: NAG.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.65, A:Y.115, A:E.130, A:R.241, A:Q.291 NAG.2: 3 residues within 4Å: Chain A: P.114, P.283 Ligands: NAG.1 No protein-ligand interaction detected (PLIP)

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

EDO.3: 3 residues within 4Å: Chain A: D.318, A.320, T.357 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.318 EDO.4: 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.5: 6 residues within 4Å: Chain A: D.612, Q.616, Q.693, S.711, S.712, I.713 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.616, A:I.713 EDO.6: 7 residues within 4Å: Chain A: W.726, M.727, R.728, R.730, M.736, D.739, P.740 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.728, A:D.739, A:E.803 Water bridges: A:M.727 EDO.20: 5 residues within 4Å: Chain A: I.501, G.506, F.765, Q.768, T.769 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.768

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

FMT.7: 5 residues within 4Å: Chain A: Y.646, E.648, D.649, G.684, Q.685 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.685 FMT.8: 6 residues within 4Å: Chain A: F.615, M.727, R.728, V.729 Chain B: P.42, S.61 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.729 FMT.9: 4 residues within 4Å: Chain A: A.534, E.535, L.572 Ligands: FMT.10 No protein-ligand interaction detected (PLIP) FMT.10: 6 residues within 4Å: Chain A: E.535, W.536, P.568, E.569, L.572 Ligands: FMT.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.536, A:E.569, A:E.569 FMT.11: 5 residues within 4Å: Chain A: I.692, Q.693, R.725, M.727, F.744 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.693 FMT.12: 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:K.633 Water bridges: A:K.633 FMT.13: 3 residues within 4Å: Chain A: F.286, R.290, F.636 No protein-ligand interaction detected (PLIP) FMT.14: 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.15: 3 residues within 4Å: Chain A: N.5, F.462, V.467 No protein-ligand interaction detected (PLIP)

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

PG4.16: 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, A:E.825, A:R.827 PG4.17: 4 residues within 4Å: Chain A: N.333, R.611, D.612, F.615 No protein-ligand interaction detected (PLIP) PG4.25: 7 residues within 4Å: Chain A: Q.831, I.840 Chain B: C.27, D.28, C.29, K.30, P.42 No protein-ligand interaction detected (PLIP)

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

P6G.18: 7 residues within 4Å: Chain A: S.651, S.654, I.655, E.656, D.657, Y.681, T.703 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.656 P6G.19: 12 residues within 4Å: Chain A: R.17, Q.18, S.20, I.21, P.27, Y.28, H.48, V.50, M.144, A.145, F.146, E.147 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.48

1 x TAR: D(-)-TARTARIC ACID(Non-covalent)

TAR.21: 7 residues within 4Å: Chain A: P.84, D.85, T.426, P.428, R.431, Y.476, Y.491 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.85, A:D.85, A:R.431, A:Y.476, A:Y.491 Salt bridges: A:R.431

1 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.22: 16 residues within 4Å: Chain A: W.314, D.342, I.343, I.379, W.416, W.453, D.455, M.456, R.515, W.528, G.530, D.531, D.560, F.564, R.587, H.589 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:D.342, A:D.342, A:W.416, A:D.455, A:R.515, A:D.531, A:D.531, A:H.589 Water bridges: A:D.531, A:D.531, A:D.531 Salt bridges: A:R.515

2 x CA: CALCIUM ION(Non-covalent)

CA.23: 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.24: 7 residues within 4Å: Chain B: R.62, N.64, 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
C

B
D

Neutral alpha-glucosidase AB

Glucosidase 2 subunit beta

Related Entries With Identical Sequence