SMTL ID : 5nn8.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 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: 3 residues within 4Å: Chain A: E.59, N.60, T.73 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.5: 3 residues within 4Å: Chain A: G.571, N.572, L.600 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.600

2 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.2: 6 residues within 4Å: Chain A: P.137, H.143, V.150, N.153, T.155, V.156 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 6 residues within 4Å: Chain A: N.390, T.392, Q.394, P.395, I.397, D.451 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.3: 5 residues within 4Å: Chain A: I.303, Q.306, V.307, N.310, Y.605 No protein-ligand interaction detected (PLIP)

1 x GLC- GLC- AC1: 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose

GLC-GLC-AC1.6: 16 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, W.538, F.569, L.570, H.594 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.296, A:W.401, A:F.569 Hydrogen bonds: A:D.202, A:D.438, A:D.438, A:R.520, A:R.520, A:D.536, A:H.594, A:H.594 Water bridges: A:D.536, A:D.536

1 x GLC- AC1: 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose(Non-covalent)

GLC-AC1.7: 7 residues within 4Å: Chain A: D.11, A.13, G.43, Q.44, P.45, W.46, C.47 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.46, A:W.46 Hydrogen bonds: A:D.11, A:D.11, A:G.43, A:W.46, A:C.47, A:C.47

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

SO4.8: 5 residues within 4Å: Chain A: H.637, E.786, V.787, L.788, E.789 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.786, A:V.787, A:L.788, A:E.789 Salt bridges: A:H.637 SO4.9: 3 residues within 4Å: Chain A: S.540, W.541, E.542 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.541, A:E.542 SO4.10: 4 residues within 4Å: Chain A: Q.677, K.680, V.683, T.684 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.677, A:T.684, A:T.684, A:T.684 Salt bridges: A:K.680

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

CL.11: 3 residues within 4Å: Chain A: R.109, Y.111, S.486 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain A: Q.20, Y.30 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain A: S.656, W.724 Ligand excluded by PLIP

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

EDO.14: 5 residues within 4Å: Chain A: V.660, D.661, H.662, Q.663, W.724 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.661, A:D.661, A:D.661, A:H.662 Water bridges: A:T.684 EDO.15: 2 residues within 4Å: Chain A: K.399, F.445 No protein-ligand interaction detected (PLIP) EDO.16: 4 residues within 4Å: Chain A: D.83, I.84, L.85, T.86 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.83, A:L.85, A:T.86 EDO.17: 3 residues within 4Å: Chain A: N.839, Q.866, L.868 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.839 EDO.18: 4 residues within 4Å: Chain A: P.173, S.174, Q.175, P.246 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.173, A:Q.175 EDO.19: 2 residues within 4Å: Chain A: R.383, R.384 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.383, A:R.383, A:R.384 EDO.20: 4 residues within 4Å: Chain A: D.90, M.92, T.102, K.104 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.90, A:K.104 Water bridges: A:D.90 EDO.21: 2 residues within 4Å: Chain A: H.719, Q.723 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.719, A:Q.723 EDO.22: 3 residues within 4Å: Chain A: R.295, G.297, L.597 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.597 EDO.23: 5 residues within 4Å: Chain A: G.741, E.772, A.773, R.774, L.799 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.741 EDO.24: 1 residues within 4Å: Chain A: T.831 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.831, A:T.831 EDO.25: 1 residues within 4Å: Chain A: Y.176 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.175, A:L.189 EDO.26: 1 residues within 4Å: Chain A: W.724 No protein-ligand interaction detected (PLIP) EDO.27: 2 residues within 4Å: Chain A: E.24, C.28 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.24 EDO.28: 3 residues within 4Å: Chain A: K.16, Q.22, R.26 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.16, A:Q.22, A:R.26

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.29: 6 residues within 4Å: Chain A: H.352, G.355, R.356, R.357, D.433, T.754 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.356, A:D.433

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

PGE.30: 2 residues within 4Å: Chain A: G.818, Q.820 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.820 Water bridges: A:Q.820

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roig-Zamboni, V. et al., Structure of human lysosomal acid alpha-glucosidase-a guide for the treatment of Pompe disease. Nat Commun (2017)

Release Date

2017-10-25

Peptides

Lysosomal alpha-glucosidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysosomal alpha-glucosidase

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