SMTL ID : 8cb1.1

Crystal structure of human lysosomal acid-alpha-glucosidase, GAA, in complex with N-PNT-DNM 15

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- BMA- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-FUC.1: 2 residues within 4Å: Chain A: E.59, N.60 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 5 residues within 4Å: Chain B: P.14, V.27, N.30, T.32, V.33 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.14 Water bridges: B:S.11 NAG-NAG.3: 5 residues within 4Å: Chain B: I.180, Q.183, V.184, N.187, Y.482 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA.4: 7 residues within 4Å: Chain B: N.267, E.268, T.269, Q.271, P.272, I.274, D.328 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.328

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.5: 2 residues within 4Å: Chain B: N.449, L.477 No protein-ligand interaction detected (PLIP)

10 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 1 residues within 4Å: Chain A: R.26 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain A: Q.20 Ligand excluded by PLIP CL.17: 1 residues within 4Å: Chain B: S.363 Ligand excluded by PLIP CL.18: 1 residues within 4Å: Chain B: F.361 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain B: S.533, W.601 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain B: S.715, V.736, S.737 Ligand excluded by PLIP CL.21: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.22: 1 residues within 4Å: Chain B: W.601 Ligand excluded by PLIP CL.23: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain B: K.494, D.609, T.610, I.611 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 5 residues within 4Å: Chain A: D.11, A.13, P.45, W.46, C.47 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.11, A:W.46, A:C.47, A:C.47 GOL.25: 7 residues within 4Å: Chain B: F.211, R.253, P.254, M.299, E.302, F.303, Q.306 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.302, B:E.302, B:Q.306 Water bridges: B:R.253 GOL.26: 3 residues within 4Å: Chain B: R.260, R.261, T.291 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.260, B:R.261 Water bridges: B:R.260 GOL.27: 5 residues within 4Å: Chain B: H.229, G.232, R.233, R.234, T.631 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.232, B:G.232 Water bridges: B:H.229, B:H.229

3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.9: 3 residues within 4Å: Chain A: Q.1, G.27, C.28 No protein-ligand interaction detected (PLIP) PGE.28: 2 residues within 4Å: Chain B: L.739, E.742 2 PLIP interactions: 2 interactions with chain B Water bridges: B:N.716, B:L.739 PGE.29: 4 residues within 4Å: Chain B: Q.635, P.637, G.695, Q.697 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.697

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

EDO.10: 5 residues within 4Å: Chain A: C.2, E.24, C.29, Y.30, I.31 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.24, A:Y.30 Water bridges: A:Y.30 EDO.11: 4 residues within 4Å: Chain A: T.102, K.104, E.112 Chain B: D.135 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.104, A:E.112 EDO.30: 2 residues within 4Å: Chain B: W.415, L.447 No protein-ligand interaction detected (PLIP) EDO.31: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.32: 3 residues within 4Å: Chain B: H.381, R.405, Y.406 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.405, B:R.405 Water bridges: B:H.381

1 x U4X: (2R,3R,4R,5S)-2-(hydroxymethyl)-1-[5-(phenanthren-9-ylmethoxy)pentyl]piperidine-3,4,5-triol(Non-covalent)

U4X.12: 15 residues within 4Å: Chain B: W.173, D.201, L.202, I.238, W.278, W.313, D.315, M.316, F.322, R.397, W.410, D.413, F.446, H.471, L.474 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:W.278, B:F.322, B:F.322, B:L.474 Hydrogen bonds: B:D.201, B:D.315, B:D.315, B:R.397, B:D.413, B:H.471 Water bridges: B:D.413, B:D.413 Salt bridges: B:D.201, B:D.315, B:D.413 pi-Stacking: B:W.278

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.13: 5 residues within 4Å: Chain B: H.514, E.663, V.664, L.665, E.666 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.663, B:V.664, B:L.665, B:E.666 Water bridges: B:H.514, B:E.666 Salt bridges: B:H.514 SO4.14: 4 residues within 4Å: Chain B: Q.554, K.557, V.560, T.561 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.554, B:T.561, B:T.561 Salt bridges: B:K.557 SO4.15: 5 residues within 4Å: Chain B: G.567, T.568, A.617, T.645, K.646 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.568, B:T.568, B:K.646 Water bridges: B:G.647 SO4.16: 3 residues within 4Å: Chain B: S.417, W.418, E.419 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.418, B:E.419 Water bridges: B:E.419

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

van der Gracht, D. et al., Fluorescence polarisation activity-based protein profiling for the identification of deoxynojirimycin-type inhibitors selective for lysosomal retaining alpha- and beta-glucosidases. Chem Sci (2023)

Release Date

2023-09-13

Peptides

Lysosomal alpha-glucosidase (76 kDa): A
Lysosomal alpha-glucosidase (70 kDa): B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
A

Lysosomal alpha-glucosidase (76 kDa)

Lysosomal alpha-glucosidase (70 kDa)

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