SMTL ID : 3hg3.1

Human alpha-galactosidase catalytic mechanism 2. Substrate bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 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.1: 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 Water bridges: A:R.7 Hydrogen bonds: A:D.2 NAG-NAG-BMA-MAN.4: 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 Water bridges: B:R.7, B:R.7 Hydrogen bonds: B:D.2, B:D.2

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.2: 4 residues within 4Å: Chain A: N.184, T.186, E.187, Q.190 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.190

2 x GLC- GLA: alpha-D-galactopyranose-(1-6)-alpha-D-glucopyranose(Non-covalent)

GLC-GLA.3: 10 residues within 4Å: Chain A: W.16, D.61, D.62, Y.103, C.111, A.112, K.137, E.172, R.196, D.200 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.62, A:D.62, A:A.112, A:K.137, A:K.137, A:E.172, A:R.196, A:R.196, A:D.200 Water bridges: A:Y.176, A:Y.176 GLC-GLA.5: 11 residues within 4Å: Chain B: W.16, D.61, D.62, Y.103, C.111, A.112, K.137, E.172, R.196, D.200 Ligands: 2PE.11 4 PLIP interactions: 4 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 Water bridges: B:Y.176, B:Y.176, B:Y.176, B:Y.176

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

NAG.6: 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:N.148 Water bridges: A:D.144 NAG.12: 6 residues within 4Å: Chain B: N.108, F.118, Y.142, C.143, D.144, N.148 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.118, B:N.148 Hydrogen bonds: B:N.108, B:D.144, B:N.148 NAG.13: 3 residues within 4Å: Chain B: N.184, E.187, Q.190 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.184, B:N.184, B:E.187, B:Q.190, B:Q.190

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

2PE.7: 11 residues within 4Å: Chain A: L.175, W.178, N.197, F.198, A.199, D.200, K.206, S.207, S.210, I.211, W.214 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.199, A:K.206, A:S.210 2PE.8: 8 residues within 4Å: Chain A: L.23, M.65, A.66, P.67, D.78, Q.80, R.81, F.114 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.65, A:Q.80, A:R.81 Water bridges: A:R.81 2PE.9: 5 residues within 4Å: Chain A: Q.219, E.220, V.223, Y.298, Q.299 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.219 Water bridges: A:Q.219, A:D.224, A:L.300 2PE.10: 8 residues within 4Å: Chain A: F.242, L.244, S.245, W.246 Chain B: L.244, S.245, W.246, N.247 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.241, A:W.246, B:W.246, B:N.247 Water bridges: A:Q.249 2PE.11: 9 residues within 4Å: Chain A: N.305, R.325, Q.326, E.327, I.328 Chain B: A.199, D.200, D.202 Ligands: GLC-GLA.5 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.305, A:E.327, B:D.202 Water bridges: A:K.209

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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