SMTL ID : 3hg5.1

Human alpha-galactosidase catalytic mechanism 4. Product bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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.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 Hydrogen bonds: A:D.2

1 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.2: 7 residues within 4Å: Chain B: D.2, N.3, G.4, R.7, N.161, G.164, R.165 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.3: 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 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.10: 5 residues within 4Å: Chain B: N.108, F.118, Y.142, C.143, N.148 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.118

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 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.62, A:D.62, A:K.137, A:K.137, A:E.172, A:R.196, A:R.196, A:D.200, A:D.200 GLA.11: 12 residues within 4Å: Chain B: W.16, D.61, D.62, Y.103, C.111, A.112, K.137, D.139, E.172, Y.176, R.196, D.200 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:D.62, B:D.62, B:Y.103, B:A.112, B:K.137, B:K.137, B:E.172, B:Y.176, B:R.196, B:R.196, B:D.200, B:D.200

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

SO4.6: 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 SO4.7: 5 residues within 4Å: Chain A: R.301, I.336, A.337, S.340, R.371 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.337, A:S.340 Salt bridges: A:R.301, A:R.371 SO4.13: 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 SO4.14: 4 residues within 4Å: Chain B: R.361, R.373, S.374, H.375 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.375 Salt bridges: B:R.361, B:H.375

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

ACY.8: 3 residues within 4Å: Chain A: R.361, S.374, H.375 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.361, A:H.375 Salt bridges: A:H.375 ACY.9: 4 residues within 4Å: Chain A: Q.355, P.358, V.359, R.361 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.359 Hydrogen bonds: A:Q.355 Salt bridges: A:R.361 ACY.15: 4 residues within 4Å: Chain B: Q.355, P.358, V.359, R.361 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:P.358 Hydrogen bonds: B:Q.355 Water bridges: B:H.375 Salt bridges: B:R.361 ACY.16: 2 residues within 4Å: Chain B: R.87, 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.12: 5 residues within 4Å: Chain B: Q.219, V.223, D.224, Y.298, K.343 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.219, B:D.224, B:K.343, B:K.343 Salt bridges: B:K.343

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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