SMTL ID : 3hg2.1

Human alpha-galactosidase catalytic mechanism 1. Empty active site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

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

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

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

NAG.4: 3 residues within 4Å: Chain A: N.184, E.187, Q.190 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.184, A:Q.190 NAG.8: 5 residues within 4Å: Chain B: N.108, F.118, Y.142, C.143, N.148 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.118, B:N.148 Water bridges: B:D.144 NAG.9: 3 residues within 4Å: Chain B: N.184, T.186, E.187 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.184, B:E.187

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

SO4.5: 4 residues within 4Å: Chain A: L.1, D.2, R.189, Q.190 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.2 Water bridges: A:L.1, A:P.228 Salt bridges: A:R.189 SO4.6: 5 residues within 4Å: Chain A: R.301, I.336, A.337, S.340, R.371 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.337, A:S.340, A:S.340 Salt bridges: A:R.301, A:R.371 SO4.11: 5 residues within 4Å: Chain B: R.301, I.336, A.337, S.340, R.371 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.337, B:S.340 Salt bridges: B:R.301, B:R.371

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

ACY.7: 3 residues within 4Å: Chain A: R.373, S.374, H.375 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.373, A:H.375 Salt bridges: A:H.375 ACY.12: 4 residues within 4Å: Chain B: L.1, D.2, R.189, Q.190 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.1, B:R.189 Salt bridges: B:R.189 ACY.13: 3 residues within 4Å: Chain B: R.87, G.132, R.165 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:R.87, B:H.94, B:R.165

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

GAL.10: 4 residues within 4Å: Chain B: Q.219, Y.298, Q.299, K.343 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.219, B:K.343, B:K.343 Water bridges: B:D.224, B:D.224

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guce, A.I. et al., Catalytic mechanism of human alpha-galactosidase. J.Biol.Chem. (2010)

Release Date

2009-11-24

Peptides

Alpha-galactosidase A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Alpha-galactosidase A

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