SMTL ID : 7p2z.1

Crystal structure of human lysosomal acid-alpha-glucosidase, GAA, in complex with cyclosulfamidate 4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

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 B: 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.137, V.150, N.153, T.155, V.156 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.137 NAG-NAG.3: 6 residues within 4Å: Chain B: I.303, Q.306, V.307, N.310, R.313, Y.605 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: 6 residues within 4Å: Chain B: N.390, T.392, Q.394, P.395, I.397, D.451 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.451

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

NAG-FUC.5: 2 residues within 4Å: Chain B: N.572, L.600 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.600 Hydrogen bonds: B:N.572 Water bridges: B:N.572, B:N.572

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

SO4.6: 3 residues within 4Å: Chain A: T.19, Q.20, Y.30 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.20 Water bridges: A:T.19, A:E.21 SO4.13: 5 residues within 4Å: Chain B: H.637, E.786, V.787, L.788, E.789 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.786, B:V.787, B:L.788, B:E.789 Water bridges: B:H.637 Salt bridges: B:H.637 SO4.14: 4 residues within 4Å: Chain B: Q.677, K.680, V.683, T.684 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.677, B:T.684, B:T.684 Salt bridges: B:K.680 SO4.15: 5 residues within 4Å: Chain B: G.690, T.691, A.740, T.768, K.769 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.691, B:T.691, B:K.769 Water bridges: B:G.770 SO4.16: 3 residues within 4Å: Chain B: S.540, W.541, E.542 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.541, B:E.542 Water bridges: B:E.542

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

CL.7: 2 residues within 4Å: Chain A: Q.1, C.28 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain A: R.26 Ligand excluded by PLIP CL.17: 1 residues within 4Å: Chain B: S.486 Ligand excluded by PLIP CL.18: 1 residues within 4Å: Chain B: F.484 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain B: S.656, W.724 Ligand excluded by PLIP CL.20: 1 residues within 4Å: Chain B: W.724 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain B: Q.175, Y.176 Ligand excluded by PLIP CL.22: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.23: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 6 residues within 4Å: Chain A: D.11, A.13 Chain B: Q.44, P.45, W.46, C.47 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:W.46, B:C.47, A:D.11 GOL.24: 6 residues within 4Å: Chain B: F.334, R.376, P.377, E.425, F.426, Q.429 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.425, B:Q.429 Water bridges: B:R.376, B:Q.429 GOL.25: 3 residues within 4Å: Chain B: R.383, R.384, T.414 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.383, B:R.384 Water bridges: B:R.383

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

EDO.10: 4 residues within 4Å: Chain A: C.2, E.24, C.29, Y.30 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.24, A:E.24, A:Y.30 Water bridges: A:Y.30 EDO.11: 4 residues within 4Å: Chain B: N.839, Q.866, F.867, L.868 No protein-ligand interaction detected (PLIP) EDO.26: 1 residues within 4Å: Chain B: F.445 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.445 EDO.27: 4 residues within 4Å: Chain B: V.660, D.661, H.662, W.724 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.661, B:D.661, B:H.662 EDO.28: 1 residues within 4Å: Chain B: Q.820 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.820

1 x YTW: (3~{a}~{R},4~{S},5~{S},6~{S},7~{R},7~{a}~{S})-7-(hydroxymethyl)-2,2-bis(oxidanylidene)-3~{a},4,5,6,7,7~{a}-hexahydro-3~{H}-benzo[d][1,2,3]oxathiazole-4,5,6-triol(Non-covalent)

YTW.12: 13 residues within 4Å: Chain B: W.296, D.324, L.325, I.361, W.401, W.436, D.438, R.520, W.533, D.536, F.569, H.594 Ligands: PGE.30 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:W.296 Hydrogen bonds: B:D.324, B:D.438, B:D.438, B:R.520, B:D.536, B:H.594 Water bridges: B:D.536, B:D.536

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

PGE.29: 6 residues within 4Å: Chain B: P.114, L.115, V.278, L.497, I.501, A.524 No protein-ligand interaction detected (PLIP) PGE.30: 3 residues within 4Å: Chain B: W.401, F.445 Ligands: YTW.12 1 PLIP interactions: 1 interactions with chain B Water bridges: B:W.401

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
AaA

Lysosomal alpha-glucosidase

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