SMTL ID : 9gtn.1

Crystal structure of human lysosomal acid-alpha-glucosidase, GAA, in complex with iminosugar compound 4k

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

2 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.139, N.140 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.5: 3 residues within 4Å: Chain A: G.651, N.652, L.680 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.680

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: 6 residues within 4Å: Chain A: P.217, H.223, V.230, N.233, T.235, V.236 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.217 NAG-NAG.3: 5 residues within 4Å: Chain A: I.383, Q.386, V.387, N.390, Y.685 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 A: N.470, E.471, T.472, Q.474, P.475, I.477, D.531 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.531

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

EDO.6: 5 residues within 4Å: Chain A: H.432, G.435, R.436, R.437, T.834 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.435 EDO.17: 6 residues within 4Å: Chain A: M.173, E.174, T.175, E.176, P.207, Y.209 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.173, A:Y.209 EDO.18: 1 residues within 4Å: Chain A: W.804 No protein-ligand interaction detected (PLIP) EDO.19: 4 residues within 4Å: Chain A: Q.255, Y.256, M.268, L.269 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.268 EDO.20: 2 residues within 4Å: Chain A: N.919, L.948 No protein-ligand interaction detected (PLIP) EDO.21: 3 residues within 4Å: Chain A: P.253, S.254, Q.255 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.253, A:Q.255 EDO.22: 4 residues within 4Å: Chain A: S.410, R.411, W.481, P.482 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.482 EDO.23: 4 residues within 4Å: Chain A: D.163, I.164, L.165, T.166 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.165, A:T.166, A:T.166 Water bridges: A:D.163, A:D.163 EDO.24: 2 residues within 4Å: Chain A: R.375, G.377 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.375 Water bridges: A:R.375, A:G.377 EDO.25: 5 residues within 4Å: Chain A: L.355, D.356, V.357, G.359, Y.360 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.196, A:Y.360 EDO.29: 1 residues within 4Å: Chain A: F.564 No protein-ligand interaction detected (PLIP) EDO.33: 2 residues within 4Å: Chain A: G.107, C.108 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.107

1 x 01: (2~{R},3~{R},4~{R},5~{S})-2-(2-hydroxyethyl)-2-(hydroxymethyl)piperidine-3,4,5-triol

01.7: 13 residues within 4Å: Chain A: W.376, D.404, L.405, I.441, W.481, W.516, D.518, M.519, R.600, W.613, D.616, F.649, H.674 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.376, A:F.649 Hydrogen bonds: A:D.518, A:D.518, A:R.600, A:D.616, A:H.674 Water bridges: A:G.615, A:D.616

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

SO4.8: 5 residues within 4Å: Chain A: H.717, E.866, V.867, L.868, E.869 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.866, A:V.867, A:L.868, A:E.869 Water bridges: A:H.717 Salt bridges: A:H.717 SO4.9: 4 residues within 4Å: Chain A: Q.757, K.760, V.763, T.764 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.764 Salt bridges: A:K.760 SO4.10: 2 residues within 4Å: Chain A: R.106, F.159 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.96, A:R.106 SO4.11: 3 residues within 4Å: Chain A: S.620, W.621, E.622 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.621, A:E.622 Water bridges: A:S.620, A:E.622

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

CL.12: 2 residues within 4Å: Chain A: Q.100, Y.110 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain A: S.736, W.804 Ligand excluded by PLIP CL.14: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.15: 1 residues within 4Å: Chain A: S.566 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain A: S.918, V.939, S.940 Ligand excluded by PLIP

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.26: 7 residues within 4Å: Chain A: F.414, R.456, P.457, M.502, E.505, F.506, Q.509 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.505, A:E.505, A:Q.509 Water bridges: A:R.456 GOL.31: 3 residues within 4Å: Chain A: R.463, R.464, T.494 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.463, A:R.463, A:R.464 Water bridges: A:T.494 GOL.32: 6 residues within 4Å: Chain A: D.91, A.93, Q.124, P.125, W.126, C.127 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.91, A:W.126, A:C.127

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

PGE.27: 2 residues within 4Å: Chain A: F.525, I.526 No protein-ligand interaction detected (PLIP) PGE.28: 3 residues within 4Å: Chain A: Q.838, Q.839, Q.900 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.839, A:Q.900 PGE.34: 6 residues within 4Å: Chain A: P.194, E.196, F.490, T.491, T.578, I.581 No protein-ligand interaction detected (PLIP)

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.30: 6 residues within 4Å: Chain A: D.170, M.172, T.182, K.184, E.192, D.338 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.170, A:K.184, A:E.192

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vieira Da Cruz, A. et al., C -Branched Iminosugars as Selective Pharmacological Chaperones of Lysosomal alpha-Glucosidase for the Treatment of Pompe Disease. J.Med.Chem. (2025)

Release Date

2025-10-01

Peptides

Lysosomal alpha-glucosidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysosomal alpha-glucosidase

Related Entries With Identical Sequence