SMTL ID : 8cb6.1

Crystal structure of human lysosomal acid-alpha-glucosidase, GAA, in covalent complex with TAMRA tagged 1,6-Epi-cylcophellitol aziridine activity based probe

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-1-1-mer

Ligands

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.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 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.14 NAG-NAG.3: 6 residues within 4Å: Chain B: I.180, Q.183, V.184, N.187, R.190, 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

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

CL.5: 1 residues within 4Å: Chain A: Q.20 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: K.16, R.26 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: P.81, K.82 Ligand excluded by PLIP CL.18: 1 residues within 4Å: Chain B: S.363 Ligand excluded by PLIP CL.19: 1 residues within 4Å: Chain B: F.361 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain B: S.533, W.601 Ligand excluded by PLIP CL.21: 1 residues within 4Å: Chain B: Q.52 Ligand excluded by PLIP CL.22: 1 residues within 4Å: Chain B: W.601 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain B: L.23, P.142 Ligand excluded by PLIP CL.24: 1 residues within 4Å: Ligands: EDO.29 Ligand excluded by PLIP

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

EDO.8: 4 residues within 4Å: Chain A: D.83, I.84, L.85, T.86 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.83, A:L.85, A:T.86, A:T.86 EDO.10: 5 residues within 4Å: Chain A: C.2, E.24, C.29, Y.30, I.31 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.24, A:Y.30 EDO.11: 5 residues within 4Å: Chain A: N.60, S.62, T.69, A.70, T.71 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.60, A:T.69 EDO.25: 2 residues within 4Å: Chain B: N.716, L.745 No protein-ligand interaction detected (PLIP) EDO.26: 3 residues within 4Å: Chain B: P.50, S.51, Q.52 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.50, B:Q.52 EDO.27: 3 residues within 4Å: Chain B: V.537, D.538, H.539 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.538, B:D.538, B:H.539 EDO.29: 2 residues within 4Å: Chain B: E.742 Ligands: CL.24 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.742 EDO.32: 7 residues within 4Å: Chain B: T.568, Y.570, A.594, H.596, G.705, T.729, K.730 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.596, B:T.729 Water bridges: B:G.705 EDO.33: 5 residues within 4Å: Chain B: H.229, G.232, R.233, R.234, T.631 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.631 Water bridges: B:H.229, B:H.229 EDO.34: 3 residues within 4Å: Chain B: Q.226, H.229, P.308 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.229

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 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.28: 6 residues within 4Å: Chain A: R.110 Chain B: D.40, G.131, G.132, L.335, N.367 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.40, B:G.132, B:N.367, B:N.367 Water bridges: A:Y.111 GOL.30: 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.31: 7 residues within 4Å: Chain B: F.211, R.253, P.254, M.299, E.302, F.303, Q.306 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.302, B:Q.306 Water bridges: B:R.253, B:E.302, B:Q.306

1 x U54: (1S,2R,3R,4R,5R)-5-[8-[4-(4-azanylbutyl)-1,2,3-triazol-1-yl]octylamino]-4-(hydroxymethyl)cyclohexane-1,2,3-triol(Covalent)

U54.12: 17 residues within 4Å: Chain B: W.173, D.201, L.202, I.238, K.276, V.277, W.278, G.280, W.313, D.315, M.316, F.322, R.397, W.410, D.413, F.446, H.471 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:K.276, B:W.278, B:D.315, B:F.322, B:F.322 Hydrogen bonds: B:W.278, B:G.280, B:D.315, B:R.397, B:D.413, B:H.471 Water bridges: B:D.413, B:D.413, B:D.413, B:D.413

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

NAG.13: 2 residues within 4Å: Chain B: N.449, L.477 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.449 Water bridges: B:N.449

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

SO4.14: 3 residues within 4Å: Chain B: S.417, W.418, E.419 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:W.418, B:E.419 Water bridges: B:S.417, B:S.417 SO4.15: 5 residues within 4Å: Chain B: H.514, E.663, V.664, L.665, E.666 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.663, B:V.664, B:L.665, B:E.666 Water bridges: B:H.514 Salt bridges: B:H.514 SO4.16: 4 residues within 4Å: Chain B: Q.554, K.557, V.560, T.561 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.554, B:T.561, B:T.561 SO4.17: 4 residues within 4Å: Chain B: T.568, A.617, T.645, K.646 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.568, B:T.568, B:K.646 Water bridges: B:A.617, B:G.647

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

PGE.35: 4 residues within 4Å: Chain B: D.79, L.80, A.81, D.413 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.81 Water bridges: B:D.413, B:D.413

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
F

B
A

Lysosomal alpha-glucosidase (76 kDa)

Lysosomal alpha-glucosidase (70 kDa)

Related Entries With Identical Sequence