SMTL ID : 3s5z.1

Pharmacological Chaperoning in Human alpha-Galactosidase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG- BMA- XYP- MAN- MAN- FUC: beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)][alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-XYP-MAN-MAN-FUC.1: 7 residues within 4Å: Chain A: D.2, N.3, G.4, R.7, N.161, G.164, R.165 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.7 Water bridges: A:D.2

1 x NAG- FUC- NAG: alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-FUC-NAG.2: 3 residues within 4Å: Chain A: N.184, T.186, E.187 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- XYP- MAN: beta-D-xylopyranose-(1-2)-[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-XYP-MAN.3: 7 residues within 4Å: Chain B: D.2, N.3, G.4, R.7, N.161, G.164, R.165 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.7, B:D.2, B:R.7 Water bridges: B:R.7

1 x NAG- NAG- BMA- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-FUC.4: 2 residues within 4Å: Chain B: N.184, T.186 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.186

2 x GLA: alpha-D-galactopyranose(Non-covalent)

GLA.5: 12 residues within 4Å: Chain A: W.16, D.61, D.62, Y.103, C.111, A.112, K.137, D.139, E.172, Y.176, R.196, D.200 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:D.62, A:D.62, A:A.112, A:K.137, A:K.137, A:Y.176, A:R.196, A:R.196, A:D.200, A:D.200 GLA.8: 11 residues within 4Å: Chain B: W.16, D.61, D.62, Y.103, C.111, A.112, K.137, D.139, E.172, R.196, D.200 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:D.62, B:Y.103, B:A.112, B:K.137, B:K.137, B:E.172, B:R.196, B:R.196, B:D.200, B:D.200

2 x GAL: beta-D-galactopyranose(Non-covalent)

GAL.6: 6 residues within 4Å: Chain A: Q.219, E.220, V.223, D.224, Y.298, K.343 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.219, A:E.220, A:D.224, A:K.343, A:K.343 Water bridges: A:K.295 Salt bridges: A:K.343 GAL.9: 6 residues within 4Å: Chain B: Q.219, E.220, V.223, D.224, Y.298, K.343 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.219, B:D.224, B:K.343, B:K.343 Water bridges: B:D.224, B:D.224 Salt bridges: B:K.343

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

NAG.7: 3 residues within 4Å: Chain B: N.108, F.118, Y.120 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 3 residues within 4Å: Chain B: L.363, F.365, Y.366 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.365

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guce, A.I. et al., The molecular basis of pharmacological chaperoning in human alpha-galactosidase. Chem.Biol. (2011)

Release Date

2012-01-04

Peptides

Alpha-galactosidase A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Alpha-galactosidase A

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