SMTL ID : 5nn5.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 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.59, N.60 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.5: 2 residues within 4Å: Chain A: N.572, L.600 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.600

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.2: 6 residues within 4Å: Chain A: P.137, I.141, 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: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.3: 6 residues within 4Å: Chain A: I.303, Q.306, V.307, N.310, R.313, Y.605 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.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 NOJ: 1-DEOXYNOJIRIMYCIN(Non-covalent)

NOJ.6: 12 residues within 4Å: Chain A: W.296, D.324, L.325, I.361, W.436, D.438, M.439, R.520, W.533, D.536, F.569, H.594 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.438, A:D.438, A:R.520, A:D.536, A:H.594 Water bridges: A:D.536, A:D.536

4 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: 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: 3 residues within 4Å: Chain A: K.16, R.26, F.79 3 PLIP interactions: 3 interactions with chain A Water bridges: A:F.79 Salt bridges: A:K.16, A:R.26 SO4.10: 4 residues within 4Å: Chain A: Q.677, K.680, V.683, T.684 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.677, A:T.684, A:T.684

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

CL.11: 3 residues within 4Å: Chain A: T.19, Q.20, Y.30 Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain A: S.486 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain A: R.144, L.146, P.265 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain A: S.838, V.859, S.860 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain A: S.656, W.724 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain A: G.43, W.193 Ligand excluded by PLIP

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

EDO.17: 5 residues within 4Å: Chain A: M.93, T.95, E.96, P.127, Y.129 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.93 EDO.18: 1 residues within 4Å: Chain A: R.383 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.383, A:R.383 Water bridges: A:R.384 EDO.19: 3 residues within 4Å: Chain A: T.691, T.768, K.769 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.691, A:T.691, A:K.769 EDO.20: 4 residues within 4Å: Chain A: A.124, S.126, P.127, L.128 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.127 EDO.21: 1 residues within 4Å: Chain A: W.724 No protein-ligand interaction detected (PLIP) EDO.22: 3 residues within 4Å: Chain A: Q.175, Y.176, M.188 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.176 Water bridges: A:Q.175, A:L.189 EDO.23: 1 residues within 4Å: Chain A: F.445 No protein-ligand interaction detected (PLIP)

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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