SMTL ID : 5nn4.1

Crystal structure of human lysosomal acid-alpha-glucosidase, GAA, in complex with N-acetyl-cysteine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.83 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 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, 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 SC2: N-ACETYL-L-CYSTEINE(Non-covalent)

SC2.6: 6 residues within 4Å: Chain A: H.352, Q.353, G.355, R.356, R.357, T.754 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.754 Hydrogen bonds: A:H.352, A:H.352 Salt bridges: A:H.352 SC2.7: 3 residues within 4Å: Chain A: H.662, L.676, Q.677 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.662 Water bridges: A:L.676 Salt bridges: A:H.662

4 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: 4 residues within 4Å: Chain A: Q.677, E.682, V.683, T.684 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.682, A:T.684 Salt bridges: A:K.680 SO4.10: 5 residues within 4Å: Chain A: G.690, T.691, A.740, T.768, K.769 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.691, A:T.691, A:K.769 Water bridges: A:T.691, A:A.740 SO4.11: 2 residues within 4Å: Chain A: R.26, F.79 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Q.22 Salt bridges: A:K.16, A:R.26

2 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

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

PGE.14: 3 residues within 4Å: Chain A: D.202, A.204, F.445 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.204 Water bridges: A:D.202, A:L.203, A:D.536

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.15: 5 residues within 4Å: Chain A: Q.1, E.24, G.27, C.28 Ligands: EDO.31 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.24 Water bridges: A:E.24 GOL.16: 3 residues within 4Å: Chain A: S.540, W.541, E.542 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.541, A:E.542 Water bridges: A:S.539, A:E.542

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

EDO.17: 6 residues within 4Å: Chain A: M.93, E.94, T.95, E.96, P.127, Y.129 Ligand excluded by PLIP EDO.18: 2 residues within 4Å: Chain A: R.383, R.384 Ligand excluded by PLIP EDO.19: 1 residues within 4Å: Chain A: W.724 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain A: Q.175, Y.176, L.189 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain A: P.114, L.115, E.116 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain A: E.96, A.124, S.126, P.127, L.128 Ligand excluded by PLIP EDO.23: 2 residues within 4Å: Chain A: P.81, K.82 Ligand excluded by PLIP EDO.24: 1 residues within 4Å: Chain A: N.839 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain A: P.173, S.174, Q.175, P.246 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain A: S.330, R.331, W.401, P.402 Ligand excluded by PLIP EDO.27: 4 residues within 4Å: Chain A: V.660, D.661, H.662, W.724 Ligand excluded by PLIP EDO.28: 2 residues within 4Å: Chain A: F.445, I.446 Ligand excluded by PLIP EDO.29: 4 residues within 4Å: Chain A: D.83, I.84, L.85, T.86 Ligand excluded by PLIP EDO.30: 4 residues within 4Å: Chain A: R.295, G.297, Y.298, I.303 Ligand excluded by PLIP EDO.31: 3 residues within 4Å: Chain A: E.24, G.27 Ligands: GOL.15 Ligand excluded by PLIP EDO.32: 5 residues within 4Å: Chain A: G.741, E.772, A.773, R.774, L.799 Ligand excluded by PLIP EDO.33: 1 residues within 4Å: Chain A: Q.820 Ligand excluded by PLIP EDO.34: 6 residues within 4Å: Chain A: T.117, L.275, D.276, V.277, G.279, Y.280 Ligand excluded by 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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