SMTL ID : 5nn3.1

Crystal structure of human lysosomal acid-alpha-glucosidase, GAA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 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: 2 residues within 4Å: Chain A: N.572, L.600 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.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)

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 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

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

SO4.6: 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:V.787, A:L.788, A:E.789 Water bridges: A:H.637, A:E.786, A:E.786 Salt bridges: A:H.637 SO4.7: 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

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

CL.8: 3 residues within 4Å: Chain A: S.838, V.859, S.860 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: Q.20, Y.30 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: R.144, L.146, P.265 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: V.660, D.661, H.662 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain A: W.296, F.569, S.596, L.597 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain A: V.675, L.676, Q.677 Ligand excluded by PLIP CL.14: 1 residues within 4Å: Chain A: R.26 Ligand excluded by PLIP CL.15: 1 residues within 4Å: Chain A: S.486 Ligand excluded by PLIP

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

PGE.16: 4 residues within 4Å: Chain A: D.202, L.203, A.204, F.445 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.204 Water bridges: A:D.202, A:D.536, A:D.536

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.17: 5 residues within 4Å: Chain A: T.117, D.276, V.277, G.279, Y.280 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.277, A:Y.280

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

EDO.18: 6 residues within 4Å: Chain A: M.93, E.94, T.95, E.96, P.127, Y.129 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.93, A:Y.129 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 Water bridges: A:R.384 EDO.20: 2 residues within 4Å: Chain A: Y.176, L.189 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.189 EDO.21: 4 residues within 4Å: Chain A: E.96, S.126, P.127, L.128 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.127 EDO.22: 2 residues within 4Å: Chain A: P.81, K.82 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.82 EDO.23: 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:T.691 EDO.24: 3 residues within 4Å: Chain A: N.839, Q.866, L.868 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.839, A:L.868 EDO.25: 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.26: 4 residues within 4Å: Chain A: S.330, R.331, W.401, P.402 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.402 EDO.27: 5 residues within 4Å: Chain A: D.11, P.14, R.195, R.251, Y.463 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.14, A:R.251 Water bridges: A:D.11 EDO.28: 2 residues within 4Å: Chain A: L.115, E.116 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.116 Water bridges: A:L.115

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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