SMTL ID : 5nn6.1

Crystal structure of human lysosomal acid-alpha-glucosidase, GAA, in complex with N-hydroxyethyl-1-deoxynojirimycin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 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: 3 residues within 4Å: Chain A: E.59, N.60, T.73 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 A: P.137, V.150, N.153, T.155, V.156 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.137 Water bridges: A:S.134 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 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.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.5: 3 residues within 4Å: Chain A: G.571, 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 MIG: (2R,3R,4R,5S)-1-(2-hydroxyethyl)-2-(hydroxymethyl)piperidine-3,4,5-triol(Non-covalent)

MIG.6: 13 residues within 4Å: Chain A: 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 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:D.324, A:D.438, A:D.438, A:R.520, A:D.536, A:H.594 Water bridges: A:D.536, A:D.536 Salt bridges: A:D.324, A:D.438, A:D.536

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 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.786, A:V.787, A:L.788, A:E.789 Water bridges: A:H.637, A:E.789 Salt bridges: A:H.637 SO4.8: 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 SO4.9: 2 residues within 4Å: Chain A: R.26, F.79 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.16, A:R.26 SO4.10: 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 SO4.11: 4 residues within 4Å: Chain A: 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

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

CL.12: 1 residues within 4Å: Chain A: Q.20 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain A: S.486 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain A: R.144, L.146, P.265 Ligand excluded by PLIP

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

EDO.15: 6 residues within 4Å: Chain A: M.93, E.94, T.95, E.96, P.127, Y.129 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.93, A:E.96, A:Y.129 EDO.16: 3 residues within 4Å: Chain A: L.146, D.147, G.148 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.148 EDO.17: 3 residues within 4Å: Chain A: V.660, D.661, H.662 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.661, A:D.661, A:H.662 EDO.18: 4 residues within 4Å: Chain A: H.352, G.355, R.356, R.357 No protein-ligand interaction detected (PLIP) EDO.19: 2 residues within 4Å: Chain A: F.445, I.446 No protein-ligand interaction detected (PLIP) EDO.20: 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.21: 3 residues within 4Å: Chain A: L.115, L.233, A.524 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.277, A:A.524 EDO.22: 2 residues within 4Å: Chain A: R.295, G.297 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.295, A:R.295 EDO.23: 5 residues within 4Å: Chain A: C.2, E.24, C.29, Y.30 Ligands: PGE.29 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.24, A:Y.30 EDO.24: 1 residues within 4Å: Chain A: N.839 1 PLIP interactions: 1 interactions with chain A Water bridges: A:F.867 EDO.25: 2 residues within 4Å: Chain A: Q.613, R.616 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.613, A:R.616 EDO.26: 4 residues within 4Å: Chain A: P.173, S.174, Q.175, P.246 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.173, A:Q.175 Water bridges: A:Q.175 EDO.27: 4 residues within 4Å: Chain A: Q.747, G.748, P.760, A.762 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.760 Water bridges: A:P.699, A:E.701

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

PGE.28: 6 residues within 4Å: Chain A: D.90, M.92, T.102, K.104, E.112, D.258 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.104 Water bridges: A:H.100, A:K.104, A:D.258 PGE.29: 6 residues within 4Å: Chain A: Q.1, E.24, A.25, G.27, C.28 Ligands: EDO.23 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.1, A:A.25 Water bridges: A:E.24, A:E.24 PGE.30: 1 residues within 4Å: Chain A: D.202 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.201, A:A.475 PGE.31: 2 residues within 4Å: Chain A: G.818, Q.820 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.818, A:Q.820 Water bridges: A:Q.758

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.32: 7 residues within 4Å: Chain A: F.334, R.376, P.377, M.422, E.425, F.426, Q.429 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.425, A:E.425, A:Q.429 Water bridges: A:R.376, A:Q.429 GOL.33: 5 residues within 4Å: Chain A: D.11, A.13, P.45, W.46, C.47 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.11, A:Q.44, A:W.46, A:C.47, A:C.47 GOL.34: 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.383, A:R.384

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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