SMTL ID : 7p32.1

Crystal structure of human lysosomal acid-alpha-glucosidase, GAA, in complex with cyclosulfamidate 6

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

monomer

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)

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.2: 5 residues within 4Å: Chain A: P.137, V.150, N.153, T.155, V.156 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.137

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.3: 7 residues within 4Å: Chain A: N.390, E.391, T.392, Q.394, P.395, I.397, D.451 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.451

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.4: 2 residues within 4Å: Chain A: N.572, L.600 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.600 Hydrogen bonds: A:N.572 Water bridges: A:N.572

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

NAG.5: 5 residues within 4Å: Chain A: I.303, Q.306, V.307, N.310, Y.605 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Q.306, A:V.307 Hydrogen bonds: A:Q.306, A:Q.306, A:N.310

1 x 56I: [(1R,2R,3R,4R,5S)-2-(hydroxymethyl)-3,4,5-tris(oxidanyl)cyclohexyl]sulfamic acid(Covalent)

56I.6: 14 residues within 4Å: Chain A: D.202, W.296, D.324, L.325, I.361, W.401, W.436, D.438, M.439, R.520, W.533, D.536, F.569, H.594 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:D.438 Hydrogen bonds: A:R.520, A:D.536, A:H.594, A:H.594 Water bridges: A:D.202, A:D.536, A:D.536, A:D.536 Salt bridges: A:R.520

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

SO4.7: 5 residues within 4Å: Chain A: H.637, E.786, V.787, L.788, E.789 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.786, A:V.787, A:L.788, A:E.789 Water bridges: A:H.637 Salt bridges: A:H.637 SO4.8: 4 residues within 4Å: Chain A: Q.677, K.680, V.683, T.684 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.677, A:T.684, A:T.684 Salt bridges: A:K.680 SO4.9: 3 residues within 4Å: Chain A: T.19, Q.20, Y.30 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.20 Water bridges: A:E.21 SO4.10: 5 residues within 4Å: Chain A: G.690, T.691, A.740, T.768, K.769 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.691, A:T.691, A:K.769 Water bridges: A:G.770 SO4.11: 3 residues within 4Å: Chain A: S.540, W.541, E.542 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.541, A:E.542 Water bridges: A:S.540, A:S.540

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

CL.12: 1 residues within 4Å: Chain A: S.486 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain A: F.484 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain A: Q.1, C.28 Ligand excluded by PLIP CL.15: 1 residues within 4Å: Chain A: R.26 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain A: S.656, W.724 Ligand excluded by PLIP CL.17: 1 residues within 4Å: Chain A: W.724 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain A: Q.175, Y.176 Ligand excluded by PLIP CL.19: 1 residues within 4Å: Chain A: S.860 Ligand excluded by PLIP CL.20: 1 residues within 4Å: Chain A: E.425 Ligand excluded by PLIP

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.21: 6 residues within 4Å: Chain A: F.334, R.376, P.377, E.425, F.426, Q.429 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.425, A:Q.429 Water bridges: A:R.376, A:Q.429 GOL.22: 6 residues within 4Å: Chain A: D.11, A.13, Q.44, P.45, W.46, C.47 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.11, A:W.46, A:C.47 GOL.23: 3 residues within 4Å: Chain A: R.383, R.384, T.414 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.383, A:R.384 Water bridges: A:R.383

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

EDO.24: 2 residues within 4Å: Chain A: F.445, I.446 No protein-ligand interaction detected (PLIP) EDO.25: 4 residues within 4Å: Chain A: V.660, D.661, H.662, W.724 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.661, A:D.661, A:H.662, A:H.662 EDO.26: 4 residues within 4Å: Chain A: C.2, E.24, C.29, Y.30 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.24, A:Y.30 Water bridges: A:Y.30 EDO.27: 1 residues within 4Å: Chain A: Q.820 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.820

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

PGE.28: 6 residues within 4Å: Chain A: P.114, L.115, F.410, L.497, I.501, A.524 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kok, K. et al., 1,6- epi-Cyclophellitol Cyclosulfamidate Is a Bona Fide Lysosomal alpha-Glucosidase Stabilizer for the Treatment of Pompe Disease. J.Am.Chem.Soc. (2022)

Release Date

2022-07-13

Peptides

Lysosomal alpha-glucosidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

Lysosomal alpha-glucosidase

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