SMTL ID : 5kzw.1

Crystal structure of human GAA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- FCA: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-D-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FCA.1: 3 residues within 4Å: Chain A: E.61, N.62, T.75 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: 6 residues within 4Å: Chain A: P.139, I.143, V.152, N.155, T.157, V.158 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.139 Water bridges: A:S.136 NAG-NAG.3: 6 residues within 4Å: Chain A: I.305, Q.308, V.309, N.312, R.315, Y.607 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.392, E.393, T.394, Q.396, P.397, I.399, D.453 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.453, A:D.453

1 x NAG- FCA: alpha-D-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FCA.5: 2 residues within 4Å: Chain A: N.574, L.602 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.574

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.6: 1 residues within 4Å: Chain A: N.804 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.804

2 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.7: 12 residues within 4Å: Chain A: W.298, D.326, L.327, I.363, W.438, D.440, R.522, W.535, D.538, F.571, H.596 Ligands: BGC.8 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.440, A:R.522, A:D.538, A:D.538, A:H.596 Salt bridges: A:R.522 GLC.9: 9 residues within 4Å: Chain A: D.13, A.15, M.44, G.45, Q.46, P.47, W.48, C.49 Ligands: BGC.10 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.13, A:G.45, A:W.48, A:C.49, A:C.49 Water bridges: A:Q.46

2 x BGC: beta-D-glucopyranose(Non-covalent)

BGC.8: 13 residues within 4Å: Chain A: W.298, D.326, L.327, I.363, W.438, D.440, M.441, R.522, W.535, D.538, F.571, H.596 Ligands: GLC.7 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.522, A:D.538, A:H.596 Water bridges: A:R.522, A:W.535, A:G.537, A:D.538 Salt bridges: A:R.522 BGC.10: 4 residues within 4Å: Chain A: A.19, I.20, W.48 Ligands: GLC.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.18, A:I.20

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

EDO.11: 3 residues within 4Å: Chain A: K.682, V.685, T.686 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.686, A:T.686 Water bridges: A:Q.679, A:Q.679, A:E.684, A:T.686 EDO.12: 1 residues within 4Å: Chain A: N.841 No protein-ligand interaction detected (PLIP) EDO.19: 3 residues within 4Å: Chain A: Q.3, G.29, C.30 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.30

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

PGE.13: 7 residues within 4Å: Chain A: R.90, D.92, M.94, T.104, K.106, E.114, D.260 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.104, A:K.106, A:E.114 Water bridges: A:R.90, A:D.260

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

PEG.14: 2 residues within 4Å: Chain A: F.486, L.487 No protein-ligand interaction detected (PLIP) PEG.17: 6 residues within 4Å: Chain A: R.197, T.208, G.210, G.468, V.469, V.470 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.468, A:G.472

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

SO4.15: 3 residues within 4Å: Chain A: S.542, W.543, E.544 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.543, A:E.544 SO4.16: 2 residues within 4Å: Chain A: K.18, R.28 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.18, A:R.28 SO4.18: 5 residues within 4Å: Chain A: H.639, E.788, V.789, L.790, E.791 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.789, A:L.790, A:E.791 Water bridges: A:E.788 Salt bridges: A:H.639

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deming, D.T. et al., The structure of human GAA: structural basis of Pompe disease. To be published

Release Date

2017-07-26

Peptides

Lysosomal alpha-glucosidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysosomal alpha-glucosidase

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