SMTL ID : 5hjr.1 (1 other biounit)

Murine endoplasmic reticulum alpha-glucosidase II with bound covalent intermediate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.1: 12 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, E.648 No protein-ligand interaction detected (PLIP)

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

EDO.2: 9 residues within 4Å: Chain A: F.6, K.7, R.210, L.214, V.216, M.225, A.226, L.227, W.254 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.210, A:A.226, A:A.226 Water bridges: A:K.7 EDO.3: 10 residues within 4Å: Chain A: H.194, A.195, Y.219, E.220, L.221, N.223, P.224, M.225, A.226, L.227 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.195, A:E.220, A:E.220, A:N.223, A:M.225 EDO.23: 6 residues within 4Å: Chain A: T.405, S.409, D.410, Y.411, E.412, L.470 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.412, A:E.412

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

FMT.4: 5 residues within 4Å: Chain A: K.201, T.203, G.206, E.207, P.224 Ligand excluded by PLIP FMT.5: 7 residues within 4Å: Chain A: A.534, E.535, W.536, N.567, P.568, E.569, L.572 Ligand excluded by PLIP FMT.6: 10 residues within 4Å: Chain A: E.186, H.187, V.188, R.199, L.200, K.201, V.202, I.257, S.259, T.264 Ligand excluded by PLIP FMT.7: 5 residues within 4Å: Chain A: R.429, W.433, N.436, M.437, N.442 Ligand excluded by PLIP FMT.8: 6 residues within 4Å: Chain A: V.56, E.58, R.70, I.71, D.72, R.82 Ligand excluded by PLIP FMT.9: 8 residues within 4Å: Chain A: I.655, D.657, Q.658, H.668, Q.679, V.680, Y.681, T.703 Ligand excluded by PLIP FMT.10: 6 residues within 4Å: Chain A: I.21, P.27, Y.28, H.48, M.144, A.145 Ligand excluded by PLIP FMT.11: 5 residues within 4Å: Chain A: S.197, L.198, R.199, S.654, E.656 Ligand excluded by PLIP FMT.12: 3 residues within 4Å: Chain A: M.494, R.523, F.524 Ligand excluded by PLIP FMT.13: 10 residues within 4Å: Chain A: F.623, T.626, L.627, Q.630, I.722, V.723, P.724, G.755, E.756, L.757 Ligand excluded by PLIP FMT.14: 8 residues within 4Å: Chain A: K.7, E.160, T.161, F.162, H.165, S.166, D.167, P.465 Ligand excluded by PLIP FMT.15: 4 residues within 4Å: Chain A: W.801, K.843, G.845 Chain B: D.20 Ligand excluded by PLIP FMT.16: 5 residues within 4Å: Chain A: L.796, E.797, T.798, S.847, A.849 Ligand excluded by PLIP FMT.17: 5 residues within 4Å: Chain A: F.565, K.566, H.591, D.593, T.594 Ligand excluded by PLIP FMT.19: 4 residues within 4Å: Chain A: I.692, R.725, M.727, F.744 Ligand excluded by PLIP FMT.24: 5 residues within 4Å: Chain A: E.344, G.348, K.349, D.355, R.358 Ligand excluded by PLIP FMT.26: 7 residues within 4Å: Chain B: E.71, Y.72, N.73, S.74, G.75, T.76, V.77 Ligand excluded by PLIP

1 x 5GF: 5-fluoro-beta-D-glucopyranose(Post Translational Modification)

5GF.18: 15 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, F.564, R.587, H.589 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.342, A:W.416, A:R.515, A:D.531, A:H.589 Water bridges: A:G.530, A:D.531

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

P6G.20: 10 residues within 4Å: Chain A: T.298, Y.629, H.632, K.633, Y.767, Q.768, H.771, F.773, D.791, K.793 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.633 P6G.25: 8 residues within 4Å: Chain A: P.79, R.80, Y.81, R.82, P.84, Y.476, G.477, W.479 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.80, A:R.82, A:W.479

1 x OXM: OXAMIC ACID(Non-covalent)

OXM.21: 6 residues within 4Å: Chain A: K.375, P.448, N.449, Y.451, E.508, H.763 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.451, A:E.508, A:H.763 Water bridges: A:N.449, A:Y.451 Salt bridges: A:K.375

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

TAR.22: 7 residues within 4Å: Chain A: R.313, W.314, N.315, Y.316, R.317, L.592, R.596 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.315 Salt bridges: A:R.313, A:R.596

2 x CA: CALCIUM ION(Non-covalent)

CA.27: 7 residues within 4Å: Chain B: Q.16, D.19, Y.21, C.22, D.23, D.29, E.30 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:Q.16, B:D.19, B:Y.21, B:D.23, B:D.29, B:E.30 CA.28: 7 residues within 4Å: Chain B: R.57, V.58, D.60, V.62, D.64, D.70, E.71 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:R.57, B:D.60, B:V.62, B:D.64, B:D.70, B:E.71

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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