SMTL ID : 5ief.1

Murine endoplasmic reticulum alpha-glucosidase II with N-butyl-1-deoxynojirimycin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.38 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 No protein-ligand interaction detected (PLIP)

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

FMT.2: 6 residues within 4Å: Chain A: I.747, Q.748, Y.750, R.780, M.782, F.799 No protein-ligand interaction detected (PLIP)

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 7 residues within 4Å: Chain A: V.56, E.58, R.70, I.71, D.72, R.82, I.329 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.58, A:R.70 Hydrogen bonds: A:E.58, A:D.72 Salt bridges: A:R.82

1 x NBV: (2R,3R,4R,5S)-1-BUTYL-2-(HYDROXYMETHYL)PIPERIDINE-3,4,5-TRIOL(Non-covalent)

NBV.4: 16 residues within 4Å: Chain A: W.369, D.397, I.398, I.434, W.471, W.508, D.510, M.511, F.517, R.570, W.583, D.586, D.615, F.619, R.642, H.644 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.471, A:F.517 Hydrogen bonds: A:D.397, A:D.397, A:D.510, A:R.570, A:D.586, A:D.586 Water bridges: A:R.642, A:R.642 Salt bridges: A:D.397, A:D.510, A:D.586

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

P6G.5: 8 residues within 4Å: Chain A: P.79, R.80, Y.81, R.82, P.84, Y.531, G.532, W.534 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.82 Water bridges: A:R.82 P6G.6: 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 Water bridges: A:I.710, A:E.711

2 x CA: CALCIUM ION(Non-covalent)

CA.7: 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.8: 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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