SMTL ID : 5ieg.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 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: 8 residues within 4Å: Chain A: N.65, Y.115, E.130, R.277, G.337, P.338, D.342, Q.346 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.130

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

6A9.2: 14 residues within 4Å: Chain A: F.253, W.369, D.397, I.398, I.434, W.508, D.510, M.511, F.517, R.570, W.583, D.586, F.619, H.644 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.253, A:W.369, A:F.517 Hydrogen bonds: A:D.397, A:D.510, A:D.510, A:R.570, A:H.644 Water bridges: A:R.642, A:R.642 Salt bridges: A:D.397, A:D.510, A:D.586

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

FMT.3: 4 residues within 4Å: Chain A: E.827, H.850, L.851, E.852 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.852 FMT.4: 3 residues within 4Å: Chain A: D.704, G.739, Q.740 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.740 Water bridges: A:D.704, A:D.704 FMT.5: 5 residues within 4Å: Chain A: I.747, Y.750, R.780, M.782, F.799 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.780 Water bridges: A:S.674 FMT.6: 5 residues within 4Å: Chain A: R.78, G.532, G.533, W.534 Ligands: P6G.8 No protein-ligand interaction detected (PLIP) FMT.7: 7 residues within 4Å: Chain A: A.589, E.590, W.591, N.622, P.623, E.624, L.627 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.624 Water bridges: A:W.591

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

P6G.8: 9 residues within 4Å: Chain A: P.79, R.80, Y.81, R.82, P.84, Y.531, G.532, W.534 Ligands: FMT.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.82 P6G.9: 7 residues within 4Å: Chain A: S.706, S.709, I.710, E.711, D.712, Y.736, T.758 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.706 Water bridges: A:I.710 P6G.10: 13 residues within 4Å: Chain A: R.17, Q.18, S.20, I.21, P.27, Y.28, H.48, V.50, G.142, M.144, A.145, F.146, E.147 No protein-ligand interaction detected (PLIP) P6G.14: 7 residues within 4Å: Chain A: D.85, L.87, V.88, A.89, M.549, R.578, F.579 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.578

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.11: 5 residues within 4Å: Chain A: L.851, E.852, T.853, S.902, A.904 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.853 Water bridges: A:L.851

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

PG4.12: 3 residues within 4Å: Chain A: E.880, S.881, R.882 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.880 PG4.13: 4 residues within 4Å: Chain A: N.388, D.663, R.666, F.670 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.670 Hydrogen bonds: A:R.666 Water bridges: A:N.388, A:D.663 PG4.17: 6 residues within 4Å: Chain A: Q.886, I.895 Chain B: C.27, D.28, C.29, K.30 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.886

2 x CA: CALCIUM ION(Non-covalent)

CA.15: 6 residues within 4Å: 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.16: 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

Related Entries With Identical Sequence