SMTL ID : 3s5y.1

Pharmacological Chaperoning in Human alpha-Galactosidase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.11 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: 6 residues within 4Å: Chain A: N.108, F.118, Y.142, C.143, D.144, N.148 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.144, A:N.148, A:D.144

1 x NAG- NAG- BMA- XYP- FUC: beta-D-xylopyranose-(1-2)-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-FUC.2: 8 residues within 4Å: Chain A: D.2, N.3, G.4, R.7, N.161, G.164, R.165, S.166 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.2, A:D.2, A:R.7 Water bridges: A:R.7, A:R.7

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.3: 4 residues within 4Å: Chain A: N.184, T.186, E.187, Q.190 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(Non-covalent)

NAG-NAG-BMA-XYP-MAN.4: 8 residues within 4Å: Chain B: D.2, N.3, G.4, R.7, N.161, G.164, R.165 Ligands: 2PE.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.7, B:R.7 Water bridges: B:D.2, B:D.2, B:G.4

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(Non-covalent)

NAG-NAG-BMA-FUC.5: 3 residues within 4Å: Chain B: N.184, E.187, Q.190 No protein-ligand interaction detected (PLIP)

2 x DGJ: (2R,3S,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol(Non-covalent)

DGJ.6: 11 residues within 4Å: Chain A: W.16, D.61, D.62, Y.103, C.111, K.137, D.139, E.172, Y.176, R.196, D.200 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:D.62, A:D.62, A:A.112, A:K.137, A:K.137, A:D.139, A:R.196, A:R.196, A:D.200 Water bridges: A:D.200, A:D.200 DGJ.9: 11 residues within 4Å: Chain B: W.16, D.61, D.62, Y.103, C.111, K.137, D.139, E.172, Y.176, R.196, D.200 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:D.62, B:D.62, B:A.112, B:K.137, B:K.137, B:E.172, B:R.196, B:R.196, B:D.200 Water bridges: B:D.200

5 x 2PE: NONAETHYLENE GLYCOL(Non-covalent)

2PE.7: 4 residues within 4Å: Chain A: Q.219, E.220, Y.298, Q.299 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.219, A:Q.299 Water bridges: A:E.220 2PE.10: 5 residues within 4Å: Chain B: L.158, N.161, Q.190, Y.191 Ligands: NAG-NAG-BMA-XYP-MAN.4 No protein-ligand interaction detected (PLIP) 2PE.11: 11 residues within 4Å: Chain B: L.5, E.56, H.94, G.97, L.98, K.99, D.134, T.163, R.165, S.166 Ligands: ACY.16 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.99, B:T.163, B:S.166, B:S.166 Water bridges: B:D.134 2PE.12: 7 residues within 4Å: Chain B: F.198, A.199, D.200, S.207, S.210, I.211, W.214 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.199, B:S.210 2PE.14: 4 residues within 4Å: Chain B: G.140, C.141, Y.142, C.143 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.142, B:C.143

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

NAG.8: 6 residues within 4Å: Chain B: N.108, F.118, Y.142, C.143, D.144, N.148 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.118 Hydrogen bonds: B:D.144 Water bridges: B:N.108

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

EDO.13: 2 residues within 4Å: Chain B: W.214, F.217 No protein-ligand interaction detected (PLIP)

2 x ACY: ACETIC ACID(Non-functional Binders)

ACY.15: 3 residues within 4Å: Chain B: L.1, D.2, R.189 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.1 Salt bridges: B:R.189 ACY.16: 3 residues within 4Å: Chain B: H.94, R.165 Ligands: 2PE.11 3 PLIP interactions: 3 interactions with chain B Water bridges: B:N.91 Salt bridges: B:H.94, B:R.165

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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